PDB Short entry for 2DH3 HEADER TRANSPORT PROTEIN, SIGNALING PROTEIN 21-MAR-06 2DH3 TITLE CRYSTAL STRUCTURE OF HUMAN ED-4F2HC COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4F2 CELL-SURFACE ANTIGEN HEAVY CHAIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ED4F2HC(ECTODOMAIN); COMPND 5 SYNONYM: 4F2HC, LYMPHOCYTE ACTIVATION ANTIGEN 4F2 LARGE SUBUNIT, 4F2 COMPND 6 HEAVY CHAIN ANTIGEN, CD98 ANTIGEN; COMPND 7 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: SLC3A2, MDU1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRCHIS (INVITROGEN) KEYWDS TIM-BARREL, GLYCOSIDASE LIKE, ANTIPARALLEL BETA-SHEET, GREEK KEY, ZN KEYWDS 2 INTERACTION, COORDINATION, DIMERIZATION, C-TERMINAL DOMAIN, KEYWDS 3 EXTRACELLULAR DOMAIN, TRANSPORT PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.FORT,I.FITA,M.PALACIN REVDAT 6 13-MAR-24 2DH3 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 2DH3 1 VERSN REVDAT 4 24-FEB-09 2DH3 1 VERSN REVDAT 3 16-OCT-07 2DH3 1 JRNL REVDAT 2 07-AUG-07 2DH3 1 REMARK REVDAT 1 27-MAR-07 2DH3 0 JRNL AUTH J.FORT,L.R.DE LA BALLINA,H.E.BURGHARDT,C.FERRER-COSTA, JRNL AUTH 2 J.TURNAY,C.FERRER-ORTA,I.USON,A.ZORZANO,J.FERNANDEZ-RECIO, JRNL AUTH 3 M.OROZCO,M.A.LIZARBE,I.FITA,M.PALACIN JRNL TITL THE STRUCTURE OF HUMAN 4F2HC ECTODOMAIN PROVIDES A MODEL FOR JRNL TITL 2 HOMODIMERIZATION AND ELECTROSTATIC INTERACTION WITH PLASMA JRNL TITL 3 MEMBRANE. JRNL REF J.BIOL.CHEM. V. 282 31444 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17724034 JRNL DOI 10.1074/JBC.M704524200 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 19304 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1066 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1436 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 28 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) : 49.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.67000 REMARK 3 B22 (A**2) : -1.65000 REMARK 3 B33 (A**2) : 3.31000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.461 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.346 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.166 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6649 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 5998 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9020 ; 1.186 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13988 ; 0.732 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 835 ; 5.601 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 299 ;32.970 ;24.582 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1119 ;14.795 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.890 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 997 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7450 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1324 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1157 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 5589 ; 0.159 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3119 ; 0.166 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3883 ; 0.077 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 113 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.018 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 9 ; 0.091 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 44 ; 0.139 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.098 ; 0.200 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): 5361 ; 0.306 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1708 ; 0.027 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6634 ; 0.338 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2923 ; 0.353 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2386 ; 0.571 ; 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 114 A 529 REMARK 3 RESIDUE RANGE : A 601 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): 22.5506 63.7738 48.0242 REMARK 3 T TENSOR REMARK 3 T11: -0.1352 T22: -0.1301 REMARK 3 T33: -0.2360 T12: -0.0316 REMARK 3 T13: 0.0216 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 2.3771 L22: 2.0151 REMARK 3 L33: 1.3279 L12: -0.7263 REMARK 3 L13: 0.3531 L23: -0.0678 REMARK 3 S TENSOR REMARK 3 S11: -0.0108 S12: -0.1918 S13: -0.0325 REMARK 3 S21: 0.2293 S22: 0.0083 S23: 0.0213 REMARK 3 S31: -0.0845 S32: -0.0056 S33: 0.0025 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 109 B 529 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2752 16.3452 41.0070 REMARK 3 T TENSOR REMARK 3 T11: -0.1108 T22: -0.1010 REMARK 3 T33: -0.1919 T12: -0.0261 REMARK 3 T13: -0.0076 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 2.1815 L22: 2.3806 REMARK 3 L33: 1.1911 L12: -0.4118 REMARK 3 L13: -0.3476 L23: 0.1575 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: -0.1341 S13: 0.0960 REMARK 3 S21: 0.2922 S22: 0.0333 S23: -0.0758 REMARK 3 S31: 0.0348 S32: -0.0111 S33: -0.0195 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2DH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000025411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : LIQ N2 COOLED SI-111 DOUBLE REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : KB-MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19650 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06650 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38850 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0,2M AMMONIUM SULFATE, REMARK 280 PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 34.74850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.98300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.89300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.98300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.74850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.89300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASP A 106 REMARK 465 ARG A 107 REMARK 465 TRP A 108 REMARK 465 GLY A 109 REMARK 465 SER A 110 REMARK 465 GLU A 111 REMARK 465 LEU A 112 REMARK 465 PRO A 113 REMARK 465 ASP B 106 REMARK 465 ARG B 107 REMARK 465 TRP B 108 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 ALA A 529 CA - C - O ANGL. DEV. = 42.9 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 ALA A 137 -93.93 -76.84 REMARK 500 GLN A 173 45.02 -91.86 REMARK 500 PHE A 218 -65.79 63.52 REMARK 500 VAL A 222 -70.62 -86.31 REMARK 500 ASP A 223 -83.04 20.73 REMARK 500 ASP A 272 46.54 -94.17 REMARK 500 SER A 293 -82.92 -63.36 REMARK 500 ASP A 306 79.73 -162.56 REMARK 500 THR A 310 -75.85 -139.21 REMARK 500 GLU A 312 33.28 -91.32 REMARK 500 ALA A 337 -41.78 -149.45 REMARK 500 ALA A 377 -4.38 82.97 REMARK 500 SER A 444 78.19 -110.26 REMARK 500 ALA A 445 -144.95 -90.76 REMARK 500 ASP A 457 -130.74 51.07 REMARK 500 SER A 480 103.82 1.45 REMARK 500 ASP A 481 79.21 52.06 REMARK 500 SER A 485 36.82 -89.20 REMARK 500 SER A 487 84.77 -15.30 REMARK 500 HIS B 135 76.24 -63.74 REMARK 500 LYS B 168 116.09 -33.89 REMARK 500 PHE B 218 -179.15 58.87 REMARK 500 GLN B 221 107.23 -12.03 REMARK 500 ASP B 272 38.42 -90.43 REMARK 500 SER B 282 -72.62 -77.50 REMARK 500 LEU B 284 -44.89 64.43 REMARK 500 LEU B 290 26.48 -79.17 REMARK 500 SER B 293 -152.86 64.51 REMARK 500 ASP B 296 67.95 -158.37 REMARK 500 SER B 302 48.16 -96.84 REMARK 500 ASP B 306 -48.60 -165.63 REMARK 500 ALA B 337 -42.66 -159.89 REMARK 500 ILE B 398 85.28 60.76 REMARK 500 ALA B 401 -51.69 -137.00 REMARK 500 HIS B 437 40.67 -155.21 REMARK 500 PRO B 447 120.51 -38.04 REMARK 500 ASP B 457 -110.51 38.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS B 295 ASP B 296 145.47 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 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 439 OD1 REMARK 620 2 HIS A 441 NE2 99.9 REMARK 620 3 HIS A 455 NE2 93.7 106.0 REMARK 620 4 HIS B 441 NE2 115.2 109.8 128.1 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 ZN A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DH2 RELATED DB: PDB DBREF 2DH3 A 111 529 UNP P08195 4F2_HUMAN 111 529 DBREF 2DH3 B 111 529 UNP P08195 4F2_HUMAN 111 529 SEQADV 2DH3 ASP A 106 UNP P08195 EXPRESSION TAG SEQADV 2DH3 ARG A 107 UNP P08195 EXPRESSION TAG SEQADV 2DH3 TRP A 108 UNP P08195 EXPRESSION TAG SEQADV 2DH3 GLY A 109 UNP P08195 EXPRESSION TAG SEQADV 2DH3 SER A 110 UNP P08195 EXPRESSION TAG SEQADV 2DH3 ASP B 106 UNP P08195 EXPRESSION TAG SEQADV 2DH3 ARG B 107 UNP P08195 EXPRESSION TAG SEQADV 2DH3 TRP B 108 UNP P08195 EXPRESSION TAG SEQADV 2DH3 GLY B 109 UNP P08195 EXPRESSION TAG SEQADV 2DH3 SER B 110 UNP P08195 EXPRESSION TAG SEQRES 1 A 424 ASP ARG TRP GLY SER GLU LEU PRO ALA GLN LYS TRP TRP SEQRES 2 A 424 HIS THR GLY ALA LEU TYR ARG ILE GLY ASP LEU GLN ALA SEQRES 3 A 424 PHE GLN GLY HIS GLY ALA GLY ASN LEU ALA GLY LEU LYS SEQRES 4 A 424 GLY ARG LEU ASP TYR LEU SER SER LEU LYS VAL LYS GLY SEQRES 5 A 424 LEU VAL LEU GLY PRO ILE HIS LYS ASN GLN LYS ASP ASP SEQRES 6 A 424 VAL ALA GLN THR ASP LEU LEU GLN ILE ASP PRO ASN PHE SEQRES 7 A 424 GLY SER LYS GLU ASP PHE ASP SER LEU LEU GLN SER ALA SEQRES 8 A 424 LYS LYS LYS SER ILE ARG VAL ILE LEU ASP LEU THR PRO SEQRES 9 A 424 ASN TYR ARG GLY GLU ASN SER TRP PHE SER THR GLN VAL SEQRES 10 A 424 ASP THR VAL ALA THR LYS VAL LYS ASP ALA LEU GLU PHE SEQRES 11 A 424 TRP LEU GLN ALA GLY VAL ASP GLY PHE GLN VAL ARG ASP SEQRES 12 A 424 ILE GLU ASN LEU LYS ASP ALA SER SER PHE LEU ALA GLU SEQRES 13 A 424 TRP GLN ASN ILE THR LYS GLY PHE SER GLU ASP ARG LEU SEQRES 14 A 424 LEU ILE ALA GLY THR ASN SER SER ASP LEU GLN GLN ILE SEQRES 15 A 424 LEU SER LEU LEU GLU SER ASN LYS ASP LEU LEU LEU THR SEQRES 16 A 424 SER SER TYR LEU SER ASP SER GLY SER THR GLY GLU HIS SEQRES 17 A 424 THR LYS SER LEU VAL THR GLN TYR LEU ASN ALA THR GLY SEQRES 18 A 424 ASN ARG TRP CYS SER TRP SER LEU SER GLN ALA ARG LEU SEQRES 19 A 424 LEU THR SER PHE LEU PRO ALA GLN LEU LEU ARG LEU TYR SEQRES 20 A 424 GLN LEU MET LEU PHE THR LEU PRO GLY THR PRO VAL PHE SEQRES 21 A 424 SER TYR GLY ASP GLU ILE GLY LEU ASP ALA ALA ALA LEU SEQRES 22 A 424 PRO GLY GLN PRO MET GLU ALA PRO VAL MET LEU TRP ASP SEQRES 23 A 424 GLU SER SER PHE PRO ASP ILE PRO GLY ALA VAL SER ALA SEQRES 24 A 424 ASN MET THR VAL LYS GLY GLN SER GLU ASP PRO GLY SER SEQRES 25 A 424 LEU LEU SER LEU PHE ARG ARG LEU SER ASP GLN ARG SER SEQRES 26 A 424 LYS GLU ARG SER LEU LEU HIS GLY ASP PHE HIS ALA PHE SEQRES 27 A 424 SER ALA GLY PRO GLY LEU PHE SER TYR ILE ARG HIS TRP SEQRES 28 A 424 ASP GLN ASN GLU ARG PHE LEU VAL VAL LEU ASN PHE GLY SEQRES 29 A 424 ASP VAL GLY LEU SER ALA GLY LEU GLN ALA SER ASP LEU SEQRES 30 A 424 PRO ALA SER ALA SER LEU PRO ALA LYS ALA ASP LEU LEU SEQRES 31 A 424 LEU SER THR GLN PRO GLY ARG GLU GLU GLY SER PRO LEU SEQRES 32 A 424 GLU LEU GLU ARG LEU LYS LEU GLU PRO HIS GLU GLY LEU SEQRES 33 A 424 LEU LEU ARG PHE PRO TYR ALA ALA SEQRES 1 B 424 ASP ARG TRP GLY SER GLU LEU PRO ALA GLN LYS TRP TRP SEQRES 2 B 424 HIS THR GLY ALA LEU TYR ARG ILE GLY ASP LEU GLN ALA SEQRES 3 B 424 PHE GLN GLY HIS GLY ALA GLY ASN LEU ALA GLY LEU LYS SEQRES 4 B 424 GLY ARG LEU ASP TYR LEU SER SER LEU LYS VAL LYS GLY SEQRES 5 B 424 LEU VAL LEU GLY PRO ILE HIS LYS ASN GLN LYS ASP ASP SEQRES 6 B 424 VAL ALA GLN THR ASP LEU LEU GLN ILE ASP PRO ASN PHE SEQRES 7 B 424 GLY SER LYS GLU ASP PHE ASP SER LEU LEU GLN SER ALA SEQRES 8 B 424 LYS LYS LYS SER ILE ARG VAL ILE LEU ASP LEU THR PRO SEQRES 9 B 424 ASN TYR ARG GLY GLU ASN SER TRP PHE SER THR GLN VAL SEQRES 10 B 424 ASP THR VAL ALA THR LYS VAL LYS ASP ALA LEU GLU PHE SEQRES 11 B 424 TRP LEU GLN ALA GLY VAL ASP GLY PHE GLN VAL ARG ASP SEQRES 12 B 424 ILE GLU ASN LEU LYS ASP ALA SER SER PHE LEU ALA GLU SEQRES 13 B 424 TRP GLN ASN ILE THR LYS GLY PHE SER GLU ASP ARG LEU SEQRES 14 B 424 LEU ILE ALA GLY THR ASN SER SER ASP LEU GLN GLN ILE SEQRES 15 B 424 LEU SER LEU LEU GLU SER ASN LYS ASP LEU LEU LEU THR SEQRES 16 B 424 SER SER TYR LEU SER ASP SER GLY SER THR GLY GLU HIS SEQRES 17 B 424 THR LYS SER LEU VAL THR GLN TYR LEU ASN ALA THR GLY SEQRES 18 B 424 ASN ARG TRP CYS SER TRP SER LEU SER GLN ALA ARG LEU SEQRES 19 B 424 LEU THR SER PHE LEU PRO ALA GLN LEU LEU ARG LEU TYR SEQRES 20 B 424 GLN LEU MET LEU PHE THR LEU PRO GLY THR PRO VAL PHE SEQRES 21 B 424 SER TYR GLY ASP GLU ILE GLY LEU ASP ALA ALA ALA LEU SEQRES 22 B 424 PRO GLY GLN PRO MET GLU ALA PRO VAL MET LEU TRP ASP SEQRES 23 B 424 GLU SER SER PHE PRO ASP ILE PRO GLY ALA VAL SER ALA SEQRES 24 B 424 ASN MET THR VAL LYS GLY GLN SER GLU ASP PRO GLY SER SEQRES 25 B 424 LEU LEU SER LEU PHE ARG ARG LEU SER ASP GLN ARG SER SEQRES 26 B 424 LYS GLU ARG SER LEU LEU HIS GLY ASP PHE HIS ALA PHE SEQRES 27 B 424 SER ALA GLY PRO GLY LEU PHE SER TYR ILE ARG HIS TRP SEQRES 28 B 424 ASP GLN ASN GLU ARG PHE LEU VAL VAL LEU ASN PHE GLY SEQRES 29 B 424 ASP VAL GLY LEU SER ALA GLY LEU GLN ALA SER ASP LEU SEQRES 30 B 424 PRO ALA SER ALA SER LEU PRO ALA LYS ALA ASP LEU LEU SEQRES 31 B 424 LEU SER THR GLN PRO GLY ARG GLU GLU GLY SER PRO LEU SEQRES 32 B 424 GLU LEU GLU ARG LEU LYS LEU GLU PRO HIS GLU GLY LEU SEQRES 33 B 424 LEU LEU ARG PHE PRO TYR ALA ALA HET ZN A 601 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *28(H2 O) HELIX 1 1 LYS A 116 THR A 120 5 5 HELIX 2 2 ASP A 128 GLY A 134 1 7 HELIX 3 3 ASN A 139 LYS A 144 1 6 HELIX 4 4 ARG A 146 SER A 152 1 7 HELIX 5 5 SER A 185 LYS A 199 1 15 HELIX 6 6 ASP A 223 ALA A 239 1 17 HELIX 7 7 ASP A 248 LEU A 252 5 5 HELIX 8 8 ASP A 254 SER A 270 1 17 HELIX 9 9 ASP A 283 GLU A 292 1 10 HELIX 10 10 GLU A 312 THR A 325 1 14 HELIX 11 11 LEU A 339 PHE A 343 5 5 HELIX 12 12 PRO A 345 GLN A 347 5 3 HELIX 13 13 LEU A 348 LEU A 359 1 12 HELIX 14 14 ASP A 391 PHE A 395 5 5 HELIX 15 15 ILE A 398 VAL A 402 5 5 HELIX 16 16 SER A 403 MET A 406 5 4 HELIX 17 17 THR A 407 ASP A 414 1 8 HELIX 18 18 SER A 417 GLU A 432 1 16 HELIX 19 19 PRO A 483 SER A 487 5 5 HELIX 20 20 LYS B 116 THR B 120 5 5 HELIX 21 21 ASP B 128 GLY B 134 1 7 HELIX 22 22 ASN B 139 LYS B 144 1 6 HELIX 23 23 ARG B 146 LEU B 153 1 8 HELIX 24 24 SER B 185 LYS B 199 1 15 HELIX 25 25 GLN B 221 GLY B 240 1 20 HELIX 26 26 ASP B 248 LEU B 252 5 5 HELIX 27 27 ASP B 254 SER B 270 1 17 HELIX 28 28 LEU B 284 SER B 289 1 6 HELIX 29 29 LEU B 290 GLU B 292 5 3 HELIX 30 30 THR B 310 ALA B 324 1 15 HELIX 31 31 LEU B 339 PHE B 343 5 5 HELIX 32 32 PRO B 345 GLN B 347 5 3 HELIX 33 33 LEU B 348 LEU B 359 1 12 HELIX 34 34 ASP B 391 PHE B 395 5 5 HELIX 35 35 SER B 403 MET B 406 5 4 HELIX 36 36 THR B 407 SER B 412 1 6 HELIX 37 37 SER B 417 GLU B 432 1 16 HELIX 38 38 GLU B 432 HIS B 437 1 6 SHEET 1 A 8 LEU A 298 THR A 300 0 SHEET 2 A 8 LEU A 274 GLY A 278 1 N ALA A 277 O LEU A 298 SHEET 3 A 8 GLY A 243 VAL A 246 1 N PHE A 244 O ILE A 276 SHEET 4 A 8 ARG A 202 ASP A 206 1 N LEU A 205 O GLN A 245 SHEET 5 A 8 VAL A 155 LEU A 160 1 N LEU A 160 O ILE A 204 SHEET 6 A 8 ALA A 122 ILE A 126 1 N TYR A 124 O VAL A 159 SHEET 7 A 8 THR A 362 SER A 366 1 O PHE A 365 N ARG A 125 SHEET 8 A 8 SER A 331 TRP A 332 1 N TRP A 332 O THR A 362 SHEET 1 B 2 HIS A 164 ASN A 166 0 SHEET 2 B 2 THR A 174 ILE A 179 -1 O GLN A 178 N LYS A 165 SHEET 1 C 6 PHE A 440 ALA A 442 0 SHEET 2 C 6 LEU A 449 ARG A 454 -1 O ILE A 453 N HIS A 441 SHEET 3 C 6 ARG A 461 ASN A 467 -1 O VAL A 464 N TYR A 452 SHEET 4 C 6 GLY A 520 PHE A 525 -1 O LEU A 523 N LEU A 463 SHEET 5 C 6 LYS A 491 SER A 497 -1 N ASP A 493 O ARG A 524 SHEET 6 C 6 PRO A 507 GLU A 509 -1 O LEU A 508 N ALA A 492 SHEET 1 D 2 LEU A 473 SER A 474 0 SHEET 2 D 2 LYS A 514 LEU A 515 -1 O LEU A 515 N LEU A 473 SHEET 1 E 8 LEU B 297 THR B 300 0 SHEET 2 E 8 LEU B 274 GLY B 278 1 N ALA B 277 O LEU B 298 SHEET 3 E 8 GLY B 243 VAL B 246 1 N PHE B 244 O ILE B 276 SHEET 4 E 8 ARG B 202 ASP B 206 1 N LEU B 205 O GLY B 243 SHEET 5 E 8 VAL B 155 LEU B 160 1 N LEU B 160 O ASP B 206 SHEET 6 E 8 ALA B 122 ILE B 126 1 N ILE B 126 O VAL B 159 SHEET 7 E 8 THR B 362 SER B 366 1 O PHE B 365 N ARG B 125 SHEET 8 E 8 SER B 331 TRP B 332 1 N TRP B 332 O THR B 362 SHEET 1 F 2 HIS B 164 GLN B 167 0 SHEET 2 F 2 ASP B 170 ILE B 179 -1 O ASP B 170 N GLN B 167 SHEET 1 G 6 ASP B 439 PHE B 443 0 SHEET 2 G 6 LEU B 449 HIS B 455 -1 O HIS B 455 N ASP B 439 SHEET 3 G 6 ARG B 461 ASN B 467 -1 O VAL B 464 N TYR B 452 SHEET 4 G 6 GLY B 520 PHE B 525 -1 O LEU B 523 N LEU B 463 SHEET 5 G 6 LYS B 491 SER B 497 -1 N LEU B 496 O LEU B 522 SHEET 6 G 6 SER B 506 GLU B 509 -1 O LEU B 508 N ALA B 492 SHEET 1 H 2 LEU B 473 SER B 474 0 SHEET 2 H 2 LYS B 514 LEU B 515 -1 O LEU B 515 N LEU B 473 LINK OD1 ASP A 439 ZN ZN A 601 1555 1555 2.00 LINK NE2 HIS A 441 ZN ZN A 601 1555 1555 2.11 LINK NE2 HIS A 455 ZN ZN A 601 1555 1555 2.21 LINK ZN ZN A 601 NE2 HIS B 441 1555 1555 2.10 CISPEP 1 GLY A 161 PRO A 162 0 3.35 CISPEP 2 GLY B 161 PRO B 162 0 5.78 SITE 1 AC1 4 ASP A 439 HIS A 441 HIS A 455 HIS B 441 CRYST1 69.497 101.786 121.966 90.00 90.00 90.00 P 21 21 21 8 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 0.014389 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008199 0.00000