PDB Short entry for 3EXI HEADER OXIDOREDUCTASE 16-OCT-08 3EXI TITLE CRYSTAL STRUCTURE OF THE PYRUVATE DEHYDROGENASE (E1P) COMPONENT OF TITLE 2 HUMAN PYRUVATE DEHYDROGENASE COMPLEX WITH THE SUBUNIT-BINDING DOMAIN TITLE 3 (SBD) OF E2P, BUT SBD CANNOT BE MODELED INTO THE ELECTRON DENSITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT ALPHA, SOMATIC COMPND 3 FORM, MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: E1P-ALPHA; COMPND 6 SYNONYM: PYRUVATE DEHYDROGENASE (E1P) ALPHA SUBUNIT; PDHE1-A TYPE I; COMPND 7 EC: 1.2.4.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: Y89F MUTANT UNABLE TO BIND THDP; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT BETA, COMPND 13 MITOCHONDRIAL; COMPND 14 CHAIN: B; COMPND 15 FRAGMENT: E1P-BETA; COMPND 16 SYNONYM: PYRUVATE DEHYDROGENASE (E1P) BETA SUBUNIT; PDHE1-B; COMPND 17 EC: 1.2.4.1; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDHA1, PHE1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PDHB, PHE1B; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HETEROTETRAMER; THIAMINE DIPHOSPHATE-DEPENDENT ENZYME; DISEASE KEYWDS 2 MUTATION; GLYCOLYSIS; LEIGH SYNDROME; MITOCHONDRION; OXIDOREDUCTASE; KEYWDS 3 PHOSPHOPROTEIN; ALTERNATIVE SPLICING; POLYMORPHISM; PYRUVATE; KEYWDS 4 THIAMINE PYROPHOSPHATE; TRANSIT PEPTIDE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO,R.M.WYNN,J.L.CHUANG,S.-C.TSO,M.MACHIUS,J.LI,D.T.CHUANG REVDAT 6 27-DEC-23 3EXI 1 REMARK REVDAT 5 20-OCT-21 3EXI 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3EXI 1 VERSN REVDAT 3 17-NOV-09 3EXI 1 JRNL REVDAT 2 24-FEB-09 3EXI 1 VERSN REVDAT 1 25-NOV-08 3EXI 0 JRNL AUTH M.KATO,R.M.WYNN,J.L.CHUANG,S.C.TSO,M.MACHIUS,J.LI,D.T.CHUANG JRNL TITL STRUCTURAL BASIS FOR INACTIVATION OF THE HUMAN PYRUVATE JRNL TITL 2 DEHYDROGENASE COMPLEX BY PHOSPHORYLATION: ROLE OF DISORDERED JRNL TITL 3 PHOSPHORYLATION LOOPS. JRNL REF STRUCTURE V. 16 1849 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 19081061 JRNL DOI 10.1016/J.STR.2008.10.010 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 56609 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1511 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3901 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5098 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.85000 REMARK 3 B22 (A**2) : -2.85000 REMARK 3 B33 (A**2) : 4.27000 REMARK 3 B12 (A**2) : -1.42000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.278 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5212 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7044 ; 1.733 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 659 ; 6.356 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;36.689 ;24.130 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 894 ;16.634 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;14.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 767 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3967 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3282 ; 0.882 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5268 ; 1.588 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1930 ; 2.980 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1776 ; 4.695 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -9 A 361 REMARK 3 ORIGIN FOR THE GROUP (A): -86.5420 25.2610 14.8300 REMARK 3 T TENSOR REMARK 3 T11: 0.0042 T22: -0.1196 REMARK 3 T33: -0.0817 T12: -0.0055 REMARK 3 T13: -0.0129 T23: -0.0530 REMARK 3 L TENSOR REMARK 3 L11: 0.9186 L22: 1.5247 REMARK 3 L33: 0.6663 L12: -1.1033 REMARK 3 L13: -0.1822 L23: -0.1358 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: 0.0960 S13: 0.0408 REMARK 3 S21: -0.0509 S22: 0.0039 S23: 0.0233 REMARK 3 S31: -0.1018 S32: -0.1356 S33: 0.0111 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 329 REMARK 3 ORIGIN FOR THE GROUP (A): -60.1650 -2.0290 29.1330 REMARK 3 T TENSOR REMARK 3 T11: -0.0035 T22: -0.0962 REMARK 3 T33: -0.1144 T12: -0.0060 REMARK 3 T13: -0.0776 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.1008 L22: 1.7620 REMARK 3 L33: 0.9140 L12: -0.4805 REMARK 3 L13: -0.1136 L23: -0.1272 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: -0.2229 S13: -0.0373 REMARK 3 S21: 0.2873 S22: -0.0363 S23: -0.3143 REMARK 3 S31: -0.0042 S32: 0.1241 S33: 0.0636 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3EXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000049890. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57582 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MIX THE PROTEINS WITH THE RATIO OF REMARK 280 E1P:SBD=1:2.10% PEG 6000, 1.5M NACL, 0.1M BISTRIS, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.29933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.64967 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.64967 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.29933 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -137.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.64967 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 TYR A 198 REMARK 465 GLY A 199 REMARK 465 MET A 200 REMARK 465 GLY A 201 REMARK 465 THR A 202 REMARK 465 SER A 203 REMARK 465 VAL A 204 REMARK 465 GLU A 205 REMARK 465 ARG A 206 REMARK 465 ALA A 207 REMARK 465 ALA A 208 REMARK 465 ALA A 209 REMARK 465 SER A 210 REMARK 465 ARG A 259 REMARK 465 TYR A 260 REMARK 465 HIS A 261 REMARK 465 GLY A 262 REMARK 465 HIS A 263 REMARK 465 SER A 264 REMARK 465 MET A 265 REMARK 465 SER A 266 REMARK 465 ASP A 267 REMARK 465 PRO A 268 REMARK 465 GLY A 269 REMARK 465 VAL A 270 REMARK 465 SER A 271 REMARK 465 TYR A 272 REMARK 465 ARG A 273 REMARK 465 THR A 274 REMARK 465 ARG A 275 REMARK 465 GLU A 276 REMARK 465 GLU A 277 REMARK 465 ILE A 278 REMARK 465 GLN A 279 REMARK 465 GLU A 280 REMARK 465 VAL A 281 REMARK 465 ARG A 282 REMARK 465 SER A 283 REMARK 465 LYS A 284 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU B 1 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N LEU B 1 OE2 GLU B 181 2.19 REMARK 500 O HOH B 2013 O HOH B 2133 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 232 CB CYS A 232 SG -0.106 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO B 283 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 62 81.24 -153.27 REMARK 500 ALA A 88 -123.09 -98.00 REMARK 500 LYS A 118 29.74 45.95 REMARK 500 ASP A 218 -94.67 60.22 REMARK 500 ALA B 36 -109.50 50.97 REMARK 500 SER B 121 -137.11 -127.52 REMARK 500 ALA B 125 -170.63 68.29 REMARK 500 TRP B 148 -62.45 -97.17 REMARK 500 ASN B 149 -169.79 -105.35 REMARK 500 SER B 213 -149.77 63.81 REMARK 500 ARG B 239 -51.47 72.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1001 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 160 O REMARK 620 2 ILE B 161 O 84.0 REMARK 620 3 ASP B 163 O 104.8 97.5 REMARK 620 4 HOH B2023 O 86.0 170.0 84.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 173 O REMARK 620 2 GLU B 173 OE2 75.4 REMARK 620 3 HOH B2103 O 83.1 144.2 REMARK 620 4 HOH B2166 O 93.5 64.2 146.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EXE RELATED DB: PDB REMARK 900 RELATED ID: 3EXF RELATED DB: PDB REMARK 900 RELATED ID: 3EXG RELATED DB: PDB REMARK 900 RELATED ID: 3EXH RELATED DB: PDB DBREF 3EXI A 1 361 UNP P08559 ODPA_HUMAN 30 390 DBREF 3EXI B 1 329 UNP P11177 ODPB_HUMAN 31 359 SEQADV 3EXI MET A -20 UNP P08559 EXPRESSION TAG SEQADV 3EXI GLY A -19 UNP P08559 EXPRESSION TAG SEQADV 3EXI SER A -18 UNP P08559 EXPRESSION TAG SEQADV 3EXI SER A -17 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -16 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -15 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -14 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -13 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -12 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -11 UNP P08559 EXPRESSION TAG SEQADV 3EXI SER A -10 UNP P08559 EXPRESSION TAG SEQADV 3EXI SER A -9 UNP P08559 EXPRESSION TAG SEQADV 3EXI GLY A -8 UNP P08559 EXPRESSION TAG SEQADV 3EXI LEU A -7 UNP P08559 EXPRESSION TAG SEQADV 3EXI VAL A -6 UNP P08559 EXPRESSION TAG SEQADV 3EXI PRO A -5 UNP P08559 EXPRESSION TAG SEQADV 3EXI ARG A -4 UNP P08559 EXPRESSION TAG SEQADV 3EXI GLY A -3 UNP P08559 EXPRESSION TAG SEQADV 3EXI SER A -2 UNP P08559 EXPRESSION TAG SEQADV 3EXI HIS A -1 UNP P08559 EXPRESSION TAG SEQADV 3EXI MET A 0 UNP P08559 EXPRESSION TAG SEQADV 3EXI PHE A 89 UNP P08559 TYR 118 ENGINEERED MUTATION SEQRES 1 A 382 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 382 LEU VAL PRO ARG GLY SER HIS MET PHE ALA ASN ASP ALA SEQRES 3 A 382 THR PHE GLU ILE LYS LYS CYS ASP LEU HIS ARG LEU GLU SEQRES 4 A 382 GLU GLY PRO PRO VAL THR THR VAL LEU THR ARG GLU ASP SEQRES 5 A 382 GLY LEU LYS TYR TYR ARG MET MET GLN THR VAL ARG ARG SEQRES 6 A 382 MET GLU LEU LYS ALA ASP GLN LEU TYR LYS GLN LYS ILE SEQRES 7 A 382 ILE ARG GLY PHE CYS HIS LEU CYS ASP GLY GLN GLU ALA SEQRES 8 A 382 CYS CYS VAL GLY LEU GLU ALA GLY ILE ASN PRO THR ASP SEQRES 9 A 382 HIS LEU ILE THR ALA PHE ARG ALA HIS GLY PHE THR PHE SEQRES 10 A 382 THR ARG GLY LEU SER VAL ARG GLU ILE LEU ALA GLU LEU SEQRES 11 A 382 THR GLY ARG LYS GLY GLY CYS ALA LYS GLY LYS GLY GLY SEQRES 12 A 382 SER MET HIS MET TYR ALA LYS ASN PHE TYR GLY GLY ASN SEQRES 13 A 382 GLY ILE VAL GLY ALA GLN VAL PRO LEU GLY ALA GLY ILE SEQRES 14 A 382 ALA LEU ALA CYS LYS TYR ASN GLY LYS ASP GLU VAL CYS SEQRES 15 A 382 LEU THR LEU TYR GLY ASP GLY ALA ALA ASN GLN GLY GLN SEQRES 16 A 382 ILE PHE GLU ALA TYR ASN MET ALA ALA LEU TRP LYS LEU SEQRES 17 A 382 PRO CYS ILE PHE ILE CYS GLU ASN ASN ARG TYR GLY MET SEQRES 18 A 382 GLY THR SER VAL GLU ARG ALA ALA ALA SER THR ASP TYR SEQRES 19 A 382 TYR LYS ARG GLY ASP PHE ILE PRO GLY LEU ARG VAL ASP SEQRES 20 A 382 GLY MET ASP ILE LEU CYS VAL ARG GLU ALA THR ARG PHE SEQRES 21 A 382 ALA ALA ALA TYR CYS ARG SER GLY LYS GLY PRO ILE LEU SEQRES 22 A 382 MET GLU LEU GLN THR TYR ARG TYR HIS GLY HIS SER MET SEQRES 23 A 382 SER ASP PRO GLY VAL SER TYR ARG THR ARG GLU GLU ILE SEQRES 24 A 382 GLN GLU VAL ARG SER LYS SER ASP PRO ILE MET LEU LEU SEQRES 25 A 382 LYS ASP ARG MET VAL ASN SER ASN LEU ALA SER VAL GLU SEQRES 26 A 382 GLU LEU LYS GLU ILE ASP VAL GLU VAL ARG LYS GLU ILE SEQRES 27 A 382 GLU ASP ALA ALA GLN PHE ALA THR ALA ASP PRO GLU PRO SEQRES 28 A 382 PRO LEU GLU GLU LEU GLY TYR HIS ILE TYR SER SER ASP SEQRES 29 A 382 PRO PRO PHE GLU VAL ARG GLY ALA ASN GLN TRP ILE LYS SEQRES 30 A 382 PHE LYS SER VAL SER SEQRES 1 B 329 LEU GLN VAL THR VAL ARG ASP ALA ILE ASN GLN GLY MET SEQRES 2 B 329 ASP GLU GLU LEU GLU ARG ASP GLU LYS VAL PHE LEU LEU SEQRES 3 B 329 GLY GLU GLU VAL ALA GLN TYR ASP GLY ALA TYR LYS VAL SEQRES 4 B 329 SER ARG GLY LEU TRP LYS LYS TYR GLY ASP LYS ARG ILE SEQRES 5 B 329 ILE ASP THR PRO ILE SER GLU MET GLY PHE ALA GLY ILE SEQRES 6 B 329 ALA VAL GLY ALA ALA MET ALA GLY LEU ARG PRO ILE CYS SEQRES 7 B 329 GLU PHE MET THR PHE ASN PHE SER MET GLN ALA ILE ASP SEQRES 8 B 329 GLN VAL ILE ASN SER ALA ALA LYS THR TYR TYR MET SER SEQRES 9 B 329 GLY GLY LEU GLN PRO VAL PRO ILE VAL PHE ARG GLY PRO SEQRES 10 B 329 ASN GLY ALA SER ALA GLY VAL ALA ALA GLN HIS SER GLN SEQRES 11 B 329 CYS PHE ALA ALA TRP TYR GLY HIS CYS PRO GLY LEU LYS SEQRES 12 B 329 VAL VAL SER PRO TRP ASN SER GLU ASP ALA LYS GLY LEU SEQRES 13 B 329 ILE LYS SER ALA ILE ARG ASP ASN ASN PRO VAL VAL VAL SEQRES 14 B 329 LEU GLU ASN GLU LEU MET TYR GLY VAL PRO PHE GLU PHE SEQRES 15 B 329 PRO PRO GLU ALA GLN SER LYS ASP PHE LEU ILE PRO ILE SEQRES 16 B 329 GLY LYS ALA LYS ILE GLU ARG GLN GLY THR HIS ILE THR SEQRES 17 B 329 VAL VAL SER HIS SER ARG PRO VAL GLY HIS CYS LEU GLU SEQRES 18 B 329 ALA ALA ALA VAL LEU SER LYS GLU GLY VAL GLU CYS GLU SEQRES 19 B 329 VAL ILE ASN MET ARG THR ILE ARG PRO MET ASP MET GLU SEQRES 20 B 329 THR ILE GLU ALA SER VAL MET LYS THR ASN HIS LEU VAL SEQRES 21 B 329 THR VAL GLU GLY GLY TRP PRO GLN PHE GLY VAL GLY ALA SEQRES 22 B 329 GLU ILE CYS ALA ARG ILE MET GLU GLY PRO ALA PHE ASN SEQRES 23 B 329 PHE LEU ASP ALA PRO ALA VAL ARG VAL THR GLY ALA ASP SEQRES 24 B 329 VAL PRO MET PRO TYR ALA LYS ILE LEU GLU ASP ASN SER SEQRES 25 B 329 ILE PRO GLN VAL LYS ASP ILE ILE PHE ALA ILE LYS LYS SEQRES 26 B 329 THR LEU ASN ILE HET K A1001 1 HET CL A1003 1 HET K B1002 1 HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION FORMUL 3 K 2(K 1+) FORMUL 4 CL CL 1- FORMUL 6 HOH *318(H2 O) HELIX 1 1 ARG A 29 GLN A 55 1 27 HELIX 2 2 GLN A 68 GLY A 78 1 11 HELIX 3 3 ALA A 91 ARG A 98 1 8 HELIX 4 4 SER A 101 THR A 110 1 10 HELIX 5 5 ALA A 140 GLY A 156 1 17 HELIX 6 6 GLY A 168 ALA A 170 5 3 HELIX 7 7 GLN A 172 LYS A 186 1 15 HELIX 8 8 ASP A 212 ARG A 216 5 5 HELIX 9 9 ASP A 229 SER A 246 1 18 HELIX 10 10 ASP A 286 SER A 298 1 13 HELIX 11 11 SER A 302 ASP A 327 1 26 HELIX 12 12 PRO A 331 LEU A 335 5 5 HELIX 13 13 VAL B 5 ASP B 20 1 16 HELIX 14 14 GLY B 42 ARG B 51 1 10 HELIX 15 15 SER B 58 ALA B 72 1 15 HELIX 16 16 THR B 82 GLN B 88 5 7 HELIX 17 17 ALA B 89 ASN B 95 1 7 HELIX 18 18 LYS B 99 SER B 104 1 6 HELIX 19 19 ALA B 125 SER B 129 5 5 HELIX 20 20 PHE B 132 HIS B 138 1 7 HELIX 21 21 ASN B 149 ASP B 163 1 15 HELIX 22 22 PRO B 183 SER B 188 1 6 HELIX 23 23 ARG B 214 LYS B 228 1 15 HELIX 24 24 ASP B 245 ASN B 257 1 13 HELIX 25 25 GLY B 270 GLY B 282 1 13 HELIX 26 26 ALA B 284 LEU B 288 5 5 HELIX 27 27 ALA B 305 ASN B 311 1 7 HELIX 28 28 GLN B 315 ASN B 328 1 14 SHEET 1 A 2 ASP A 4 GLU A 8 0 SHEET 2 A 2 THR A 24 THR A 28 -1 O THR A 25 N PHE A 7 SHEET 1 B 6 ASP A 13 HIS A 15 0 SHEET 2 B 6 GLY A 222 ASP A 226 -1 O GLY A 222 N HIS A 15 SHEET 3 B 6 ILE A 251 THR A 257 1 O GLU A 254 N LEU A 223 SHEET 4 B 6 CYS A 189 ASN A 196 1 N PHE A 191 O ILE A 251 SHEET 5 B 6 CYS A 161 GLY A 166 1 N THR A 163 O ILE A 192 SHEET 6 B 6 HIS A 84 ILE A 86 1 N ILE A 86 O LEU A 164 SHEET 1 C 2 PHE A 346 ARG A 349 0 SHEET 2 C 2 LYS A 356 SER A 359 -1 O SER A 359 N PHE A 346 SHEET 1 D 2 GLN B 2 THR B 4 0 SHEET 2 D 2 PRO B 179 GLU B 181 -1 O PHE B 180 N VAL B 3 SHEET 1 E 7 ILE B 52 ASP B 54 0 SHEET 2 E 7 VAL B 23 GLY B 27 1 N LEU B 25 O ILE B 53 SHEET 3 E 7 ARG B 75 GLU B 79 1 O ILE B 77 N LEU B 26 SHEET 4 E 7 VAL B 113 PRO B 117 1 O VAL B 113 N CYS B 78 SHEET 5 E 7 VAL B 167 GLU B 171 1 O VAL B 169 N PHE B 114 SHEET 6 E 7 LYS B 143 VAL B 145 1 N LYS B 143 O VAL B 168 SHEET 7 E 7 THR B 240 ARG B 242 -1 O ILE B 241 N VAL B 144 SHEET 1 F 5 LYS B 199 ARG B 202 0 SHEET 2 F 5 CYS B 233 ASN B 237 -1 O ASN B 237 N LYS B 199 SHEET 3 F 5 ILE B 207 SER B 211 1 N ILE B 207 O GLU B 234 SHEET 4 F 5 LEU B 259 VAL B 262 1 O VAL B 262 N VAL B 210 SHEET 5 F 5 VAL B 293 VAL B 295 1 O VAL B 295 N THR B 261 LINK K K A1001 O ALA B 160 1555 1555 2.62 LINK K K A1001 O ILE B 161 1555 1555 2.66 LINK K K A1001 O ASP B 163 1555 1555 2.39 LINK K K A1001 O HOH B2023 1555 1555 2.40 LINK O GLU B 173 K K B1002 1555 1555 2.67 LINK OE2 GLU B 173 K K B1002 1555 1555 2.93 LINK K K B1002 O HOH B2103 1555 1555 2.45 LINK K K B1002 O HOH B2166 1555 1555 2.51 CISPEP 1 GLY A 133 GLY A 134 0 5.53 CISPEP 2 ASP B 34 GLY B 35 0 15.79 CISPEP 3 ARG B 242 PRO B 243 0 -4.83 SITE 1 AC1 5 ALA B 160 ILE B 161 ASP B 163 HOH B2023 SITE 2 AC1 5 HOH B2034 SITE 1 AC2 5 HOH A2050 HOH A2201 GLU B 173 HOH B2103 SITE 2 AC2 5 HOH B2166 SITE 1 AC3 3 ARG A 44 ARG A 314 ILE A 317 CRYST1 154.378 154.378 82.949 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006478 0.003740 0.000000 0.00000 SCALE2 0.000000 0.007480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012056 0.00000