PDB Short entry for 3K5T HEADER OXIDOREDUCTASE 08-OCT-09 3K5T TITLE CRYSTAL STRUCTURE OF HUMAN DIAMINE OXIDASE IN SPACE GROUP C2221 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMILORIDE-SENSITIVE AMINE OXIDASE [COPPER-CONTAINING], DAO, COMPND 5 AMILORIDE-BINDING PROTEIN, ABP, HISTAMINASE, KIDNEY AMINE OXIDASE, COMPND 6 KAO; COMPND 7 EC: 1.4.3.22; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ABP1, AOC1, DAO1; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: DROSOPHILA SCHNEIDER 2 (S2) KEYWDS OXIDOREDUCTASE, COPPER AMINE OXIDASE, CAO, TOPAQUINONE, TPQ, DIAMINE KEYWDS 2 OXIDASE, DAO, HUMAN, GLYCOPROTEIN, HEPARIN-BINDING, METAL-BINDING, KEYWDS 3 SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR A.P.MCGRATH,J.M.GUSS REVDAT 5 06-SEP-23 3K5T 1 REMARK REVDAT 4 13-OCT-21 3K5T 1 SEQADV HETSYN REVDAT 3 29-JUL-20 3K5T 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 28-MAR-12 3K5T 1 JRNL VERSN REVDAT 1 09-FEB-10 3K5T 0 JRNL AUTH A.P.MCGRATH,K.M.HILMER,C.A.COLLYER,D.M.DOOLEY,J.M.GUSS JRNL TITL A NEW CRYSTAL FORM OF HUMAN DIAMINE OXIDASE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 66 137 2010 JRNL REFN ESSN 1744-3091 JRNL PMID 20124708 JRNL DOI 10.1107/S1744309109052130 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 45199 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2288 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) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3042 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5587 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.95000 REMARK 3 B22 (A**2) : -1.74000 REMARK 3 B33 (A**2) : 3.70000 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): 0.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.237 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.190 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.303 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.901 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.850 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5883 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3870 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8069 ; 1.224 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9339 ; 0.820 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 716 ; 6.739 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 271 ;31.806 ;22.915 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 788 ;13.578 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;15.268 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6645 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1292 ; 0.001 ; 0.020 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): 3578 ; 0.431 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1423 ; 0.082 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5767 ; 0.777 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2305 ; 1.136 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2300 ; 1.792 ; 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 : NULL 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, U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 3K5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055582. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-07; 01-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; AUSTRALIAN REMARK 200 SYNCHROTRON REMARK 200 BEAMLINE : NULL; MX1 REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.957 REMARK 200 MONOCHROMATOR : NI FILTER; NULL REMARK 200 OPTICS : OSMIC MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; ADSC REMARK 200 QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45200 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.106 REMARK 200 RESOLUTION RANGE LOW (A) : 178.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : 0.11100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29900 REMARK 200 R SYM FOR SHELL (I) : 0.29900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2C10 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES (PH 6.1), 12% W/V PEG REMARK 280 20,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.03000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 89.03000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 47.38550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.47700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.38550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.47700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 89.03000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.38550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.47700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 89.03000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.38550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.47700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 ARG A 21 REMARK 465 SER A 22 REMARK 465 PRO A 23 REMARK 465 GLY A 24 REMARK 465 THR A 25 REMARK 465 LEU A 26 REMARK 465 ASP A 265 REMARK 465 PRO A 266 REMARK 465 LEU A 267 REMARK 465 PRO A 268 REMARK 465 GLY A 269 REMARK 465 GLY A 270 REMARK 465 LYS A 271 REMARK 465 GLY A 272 REMARK 465 HIS A 273 REMARK 465 ASP A 274 REMARK 465 SER A 275 REMARK 465 THR A 276 REMARK 465 GLU A 277 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 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 39 CG CD OE1 NE2 REMARK 470 TRP A 49 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 49 CZ3 CH2 REMARK 470 LYS A 51 CE NZ REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 ARG A 55 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 ARG A 91 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 92 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 CYS A 123 SG REMARK 470 ARG A 126 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 135 CG CD OE1 NE2 REMARK 470 HIS A 153 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 GLN A 164 CG CD OE1 NE2 REMARK 470 GLN A 175 CG CD OE1 NE2 REMARK 470 ASP A 176 CG OD1 OD2 REMARK 470 HIS A 178 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 179 CG OD1 OD2 REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 ARG A 251 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 264 CG CD OE1 OE2 REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 HIS A 362 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 436 CG CD CE NZ REMARK 470 GLU A 493 CG CD OE1 OE2 REMARK 470 LYS A 526 CG CD CE NZ REMARK 470 GLN A 533 CG CD OE1 NE2 REMARK 470 LYS A 535 CG CD CE NZ REMARK 470 ARG A 546 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 556 CG CD OE1 NE2 REMARK 470 ARG A 568 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 570 CG CD CE NZ REMARK 470 LYS A 572 CG CD CE NZ REMARK 470 LYS A 575 CD CE NZ REMARK 470 LYS A 590 CG CD CE NZ REMARK 470 ARG A 628 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 652 CG CD OE1 NE2 REMARK 470 ASN A 721 CG OD1 ND2 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 ND2 ASN A 538 O5 NAG C 1 2.18 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 THR A 62 45.97 -84.78 REMARK 500 PHE A 103 63.67 -105.00 REMARK 500 SER A 129 72.80 48.62 REMARK 500 ASP A 176 -70.02 68.27 REMARK 500 CYS A 177 -43.07 48.10 REMARK 500 HIS A 178 -88.88 40.86 REMARK 500 ARG A 197 73.51 -153.44 REMARK 500 ASN A 239 48.07 36.64 REMARK 500 ASP A 255 31.99 -98.31 REMARK 500 PRO A 279 154.39 -44.46 REMARK 500 VAL A 381 43.22 -108.36 REMARK 500 TYR A 459 -95.76 -158.43 REMARK 500 ALA A 523 23.90 47.41 REMARK 500 ASN A 541 107.98 -59.85 REMARK 500 SER A 544 78.08 -165.68 REMARK 500 GLN A 610 -108.07 59.13 REMARK 500 ASN A 657 71.10 28.48 REMARK 500 ASP A 705 108.38 -46.35 REMARK 500 ASN A 721 -64.78 -90.86 REMARK 500 ARG A 734 28.09 -142.45 REMARK 500 TYR A 748 86.94 -150.94 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 CU A 801 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPQ A 461 O4 REMARK 620 2 HIS A 510 NE2 89.5 REMARK 620 3 HIS A 512 NE2 106.3 99.8 REMARK 620 4 HIS A 675 ND1 112.2 103.1 134.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 802 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 519 OD1 REMARK 620 2 LEU A 520 O 104.2 REMARK 620 3 ASP A 521 OD1 91.0 80.3 REMARK 620 4 ASP A 664 OD1 96.9 156.7 89.7 REMARK 620 5 LEU A 665 O 85.1 90.1 168.4 101.6 REMARK 620 6 HOH A 809 O 170.6 72.1 96.8 88.5 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 803 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 562 OE1 REMARK 620 2 GLU A 562 OE2 51.9 REMARK 620 3 PHE A 653 O 92.7 109.1 REMARK 620 4 ASN A 656 OD1 90.6 136.3 92.0 REMARK 620 5 GLU A 658 OE1 102.0 78.5 165.0 90.8 REMARK 620 6 HOH A 951 O 152.6 155.3 75.1 65.9 92.6 REMARK 620 N 1 2 3 4 5 DBREF 3K5T A 21 751 UNP P19801 ABP1_HUMAN 21 751 SEQADV 3K5T ARG A 21 UNP P19801 PRO 21 ENGINEERED MUTATION SEQADV 3K5T SER A 592 UNP P19801 THR 592 VARIANT SEQADV 3K5T ASP A 645 UNP P19801 HIS 645 VARIANT SEQRES 1 A 731 ARG SER PRO GLY THR LEU PRO ARG LYS ALA GLY VAL PHE SEQRES 2 A 731 SER ASP LEU SER ASN GLN GLU LEU LYS ALA VAL HIS SER SEQRES 3 A 731 PHE LEU TRP SER LYS LYS GLU LEU ARG LEU GLN PRO SER SEQRES 4 A 731 SER THR THR THR MET ALA LYS ASN THR VAL PHE LEU ILE SEQRES 5 A 731 GLU MET LEU LEU PRO LYS LYS TYR HIS VAL LEU ARG PHE SEQRES 6 A 731 LEU ASP LYS GLY GLU ARG HIS PRO VAL ARG GLU ALA ARG SEQRES 7 A 731 ALA VAL ILE PHE PHE GLY ASP GLN GLU HIS PRO ASN VAL SEQRES 8 A 731 THR GLU PHE ALA VAL GLY PRO LEU PRO GLY PRO CYS TYR SEQRES 9 A 731 MET ARG ALA LEU SER PRO ARG PRO GLY TYR GLN SER SER SEQRES 10 A 731 TRP ALA SER ARG PRO ILE SER THR ALA GLU TYR ALA LEU SEQRES 11 A 731 LEU TYR HIS THR LEU GLN GLU ALA THR LYS PRO LEU HIS SEQRES 12 A 731 GLN PHE PHE LEU ASN THR THR GLY PHE SER PHE GLN ASP SEQRES 13 A 731 CYS HIS ASP ARG CYS LEU ALA PHE THR ASP VAL ALA PRO SEQRES 14 A 731 ARG GLY VAL ALA SER GLY GLN ARG ARG SER TRP LEU ILE SEQRES 15 A 731 ILE GLN ARG TYR VAL GLU GLY TYR PHE LEU HIS PRO THR SEQRES 16 A 731 GLY LEU GLU LEU LEU VAL ASP HIS GLY SER THR ASP ALA SEQRES 17 A 731 GLY HIS TRP ALA VAL GLU GLN VAL TRP TYR ASN GLY LYS SEQRES 18 A 731 PHE TYR GLY SER PRO GLU GLU LEU ALA ARG LYS TYR ALA SEQRES 19 A 731 ASP GLY GLU VAL ASP VAL VAL VAL LEU GLU ASP PRO LEU SEQRES 20 A 731 PRO GLY GLY LYS GLY HIS ASP SER THR GLU GLU PRO PRO SEQRES 21 A 731 LEU PHE SER SER HIS LYS PRO ARG GLY ASP PHE PRO SER SEQRES 22 A 731 PRO ILE HIS VAL SER GLY PRO ARG LEU VAL GLN PRO HIS SEQRES 23 A 731 GLY PRO ARG PHE ARG LEU GLU GLY ASN ALA VAL LEU TYR SEQRES 24 A 731 GLY GLY TRP SER PHE ALA PHE ARG LEU ARG SER SER SER SEQRES 25 A 731 GLY LEU GLN VAL LEU ASN VAL HIS PHE GLY GLY GLU ARG SEQRES 26 A 731 ILE ALA TYR GLU VAL SER VAL GLN GLU ALA VAL ALA LEU SEQRES 27 A 731 TYR GLY GLY HIS THR PRO ALA GLY MET GLN THR LYS TYR SEQRES 28 A 731 LEU ASP VAL GLY TRP GLY LEU GLY SER VAL THR HIS GLU SEQRES 29 A 731 LEU ALA PRO GLY ILE ASP CYS PRO GLU THR ALA THR PHE SEQRES 30 A 731 LEU ASP THR PHE HIS TYR TYR ASP ALA ASP ASP PRO VAL SEQRES 31 A 731 HIS TYR PRO ARG ALA LEU CYS LEU PHE GLU MET PRO THR SEQRES 32 A 731 GLY VAL PRO LEU ARG ARG HIS PHE ASN SER ASN PHE LYS SEQRES 33 A 731 GLY GLY PHE ASN PHE TYR ALA GLY LEU LYS GLY GLN VAL SEQRES 34 A 731 LEU VAL LEU ARG THR THR SER THR VAL TYR ASN TPQ ASP SEQRES 35 A 731 TYR ILE TRP ASP PHE ILE PHE TYR PRO ASN GLY VAL MET SEQRES 36 A 731 GLU ALA LYS MET HIS ALA THR GLY TYR VAL HIS ALA THR SEQRES 37 A 731 PHE TYR THR PRO GLU GLY LEU ARG HIS GLY THR ARG LEU SEQRES 38 A 731 HIS THR HIS LEU ILE GLY ASN ILE HIS THR HIS LEU VAL SEQRES 39 A 731 HIS TYR ARG VAL ASP LEU ASP VAL ALA GLY THR LYS ASN SEQRES 40 A 731 SER PHE GLN THR LEU GLN MET LYS LEU GLU ASN ILE THR SEQRES 41 A 731 ASN PRO TRP SER PRO ARG HIS ARG VAL VAL GLN PRO THR SEQRES 42 A 731 LEU GLU GLN THR GLN TYR SER TRP GLU ARG GLN ALA ALA SEQRES 43 A 731 PHE ARG PHE LYS ARG LYS LEU PRO LYS TYR LEU LEU PHE SEQRES 44 A 731 THR SER PRO GLN GLU ASN PRO TRP GLY HIS LYS ARG SER SEQRES 45 A 731 TYR ARG LEU GLN ILE HIS SER MET ALA ASP GLN VAL LEU SEQRES 46 A 731 PRO PRO GLY TRP GLN GLU GLU GLN ALA ILE THR TRP ALA SEQRES 47 A 731 ARG TYR PRO LEU ALA VAL THR LYS TYR ARG GLU SER GLU SEQRES 48 A 731 LEU CYS SER SER SER ILE TYR HIS GLN ASN ASP PRO TRP SEQRES 49 A 731 ASP PRO PRO VAL VAL PHE GLU GLN PHE LEU HIS ASN ASN SEQRES 50 A 731 GLU ASN ILE GLU ASN GLU ASP LEU VAL ALA TRP VAL THR SEQRES 51 A 731 VAL GLY PHE LEU HIS ILE PRO HIS SER GLU ASP ILE PRO SEQRES 52 A 731 ASN THR ALA THR PRO GLY ASN SER VAL GLY PHE LEU LEU SEQRES 53 A 731 ARG PRO PHE ASN PHE PHE PRO GLU ASP PRO SER LEU ALA SEQRES 54 A 731 SER ARG ASP THR VAL ILE VAL TRP PRO ARG ASP ASN GLY SEQRES 55 A 731 PRO ASN TYR VAL GLN ARG TRP ILE PRO GLU ASP ARG ASP SEQRES 56 A 731 CYS SER MET PRO PRO PRO PHE SER TYR ASN GLY THR TYR SEQRES 57 A 731 ARG PRO VAL MODRES 3K5T ASN A 110 ASN GLYCOSYLATION SITE MODRES 3K5T ASN A 538 ASN GLYCOSYLATION SITE MODRES 3K5T ASN A 745 ASN GLYCOSYLATION SITE MODRES 3K5T TPQ A 461 TYR HET TPQ A 461 14 HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET CU A 801 1 HET CA A 802 1 HET CA A 803 1 HET GOL A 804 6 HET NAG A7451 14 HETNAM TPQ 5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CU COPPER (II) ION HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN TPQ 5-(2-CARBOXY-2-AMINOETHYL)-4-HYDROXY-1,2-BENZOQUINONE; HETSYN 2 TPQ 2,4,5-TRIHYDROXYPHENYLALANINE QUINONE; TOPA QUINONE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 TPQ C9 H9 N O5 FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 4 CU CU 2+ FORMUL 5 CA 2(CA 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 9 HOH *299(H2 O) HELIX 1 1 LYS A 29 SER A 34 5 6 HELIX 2 2 SER A 37 LYS A 51 1 15 HELIX 3 3 LYS A 52 ARG A 55 5 4 HELIX 4 4 LYS A 78 ASP A 87 1 10 HELIX 5 5 SER A 144 THR A 159 1 16 HELIX 6 6 LEU A 162 GLY A 171 1 10 HELIX 7 7 GLY A 209 LEU A 212 5 4 HELIX 8 8 ASP A 227 TRP A 231 5 5 HELIX 9 9 SER A 245 ASP A 255 1 11 HELIX 10 10 THR A 363 THR A 369 1 7 HELIX 11 11 VAL A 374 GLY A 377 5 4 HELIX 12 12 THR A 491 ARG A 496 5 6 HELIX 13 13 TRP A 561 GLN A 564 5 4 HELIX 14 14 TRP A 609 TYR A 620 5 12 HELIX 15 15 VAL A 649 LEU A 654 1 6 HELIX 16 16 HIS A 678 ILE A 682 5 5 HELIX 17 17 ASP A 705 SER A 710 5 6 SHEET 1 A14 TYR A 124 ALA A 127 0 SHEET 2 A14 ASN A 110 LEU A 119 -1 N ALA A 115 O ARG A 126 SHEET 3 A14 ARG A 95 PHE A 103 -1 N ALA A 97 O VAL A 116 SHEET 4 A14 ASN A 67 MET A 74 -1 N GLU A 73 O ARG A 98 SHEET 5 A14 THR A 396 TYR A 404 -1 O TYR A 403 N ILE A 72 SHEET 6 A14 VAL A 410 PRO A 422 -1 O LEU A 416 N LEU A 398 SHEET 7 A14 GLN A 448 THR A 457 -1 O VAL A 451 N PHE A 419 SHEET 8 A14 TPQ A 461 PHE A 469 -1 O PHE A 467 N LEU A 452 SHEET 9 A14 MET A 475 GLY A 483 -1 O LYS A 478 N ASP A 466 SHEET 10 A14 SER A 691 PHE A 699 -1 O LEU A 696 N MET A 475 SHEET 11 A14 LYS A 590 HIS A 598 -1 N SER A 592 O PHE A 699 SHEET 12 A14 TYR A 576 GLU A 584 -1 N SER A 581 O ARG A 591 SHEET 13 A14 SER A 528 MET A 534 -1 N SER A 528 O THR A 580 SHEET 14 A14 LEU A 554 GLN A 558 -1 O GLU A 555 N GLN A 533 SHEET 1 B 5 LEU A 182 ASP A 186 0 SHEET 2 B 5 ARG A 198 ARG A 205 -1 O GLN A 204 N ALA A 183 SHEET 3 B 5 PRO A 214 ASP A 222 -1 O THR A 215 N ILE A 203 SHEET 4 B 5 ALA A 232 TYR A 238 -1 O TRP A 237 N GLU A 218 SHEET 5 B 5 LYS A 241 PHE A 242 -1 O LYS A 241 N TYR A 238 SHEET 1 C 6 ARG A 311 GLU A 313 0 SHEET 2 C 6 ALA A 316 TYR A 319 -1 O ALA A 316 N GLU A 313 SHEET 3 C 6 TRP A 322 ARG A 329 -1 O PHE A 324 N VAL A 317 SHEET 4 C 6 GLY A 333 PHE A 341 -1 O HIS A 340 N SER A 323 SHEET 5 C 6 GLU A 344 TYR A 359 -1 O VAL A 350 N VAL A 336 SHEET 6 C 6 LYS A 370 LEU A 372 -1 O TYR A 371 N ALA A 357 SHEET 1 D 9 ARG A 311 GLU A 313 0 SHEET 2 D 9 ALA A 316 TYR A 319 -1 O ALA A 316 N GLU A 313 SHEET 3 D 9 TRP A 322 ARG A 329 -1 O PHE A 324 N VAL A 317 SHEET 4 D 9 GLY A 333 PHE A 341 -1 O HIS A 340 N SER A 323 SHEET 5 D 9 GLU A 344 TYR A 359 -1 O VAL A 350 N VAL A 336 SHEET 6 D 9 HIS A 510 LEU A 520 -1 O HIS A 515 N GLN A 353 SHEET 7 D 9 LEU A 665 HIS A 675 -1 O PHE A 673 N HIS A 512 SHEET 8 D 9 LEU A 622 LYS A 626 -1 N THR A 625 O VAL A 666 SHEET 9 D 9 ALA A 566 PHE A 567 -1 N PHE A 567 O LEU A 622 SHEET 1 E 4 ARG A 428 SER A 433 0 SHEET 2 E 4 PHE A 439 LEU A 445 -1 O ASN A 440 N ASN A 432 SHEET 3 E 4 VAL A 714 TRP A 717 -1 O VAL A 716 N TYR A 442 SHEET 4 E 4 TYR A 725 ARG A 728 -1 O GLN A 727 N ILE A 715 SHEET 1 F 3 ALA A 487 PHE A 489 0 SHEET 2 F 3 LEU A 505 ASN A 508 -1 O ILE A 506 N THR A 488 SHEET 3 F 3 GLY A 498 HIS A 502 -1 N THR A 499 O GLY A 507 SHEET 1 G 2 GLU A 537 THR A 540 0 SHEET 2 G 2 ARG A 548 GLN A 551 -1 O VAL A 549 N ILE A 539 SSBOND 1 CYS A 177 CYS A 181 1555 1555 2.71 SSBOND 2 CYS A 391 CYS A 417 1555 1555 2.06 LINK ND2 ASN A 110 C1 NAG B 1 1555 1555 1.44 LINK C ASN A 460 N TPQ A 461 1555 1555 1.34 LINK C TPQ A 461 N ASP A 462 1555 1555 1.33 LINK ND2 ASN A 538 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 745 C1 NAG A7451 1555 1555 1.42 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 TPQ A 461 CU CU A 801 1555 1555 2.13 LINK NE2 HIS A 510 CU CU A 801 1555 1555 2.06 LINK NE2 HIS A 512 CU CU A 801 1555 1555 2.00 LINK OD1 ASP A 519 CA CA A 802 1555 1555 2.41 LINK O LEU A 520 CA CA A 802 1555 1555 2.40 LINK OD1 ASP A 521 CA CA A 802 1555 1555 2.12 LINK OE1 GLU A 562 CA CA A 803 1555 1555 2.55 LINK OE2 GLU A 562 CA CA A 803 1555 1555 2.40 LINK O PHE A 653 CA CA A 803 1555 1555 2.41 LINK OD1 ASN A 656 CA CA A 803 1555 1555 2.26 LINK OE1 GLU A 658 CA CA A 803 1555 1555 2.77 LINK OD1 ASP A 664 CA CA A 802 1555 1555 2.47 LINK O LEU A 665 CA CA A 802 1555 1555 2.32 LINK ND1 HIS A 675 CU CU A 801 1555 1555 1.80 LINK CA CA A 802 O HOH A 809 1555 1555 2.97 LINK CA CA A 803 O HOH A 951 1555 1555 2.44 CISPEP 1 GLY A 117 PRO A 118 0 -4.39 CISPEP 2 LEU A 119 PRO A 120 0 -7.20 CISPEP 3 ALA A 188 PRO A 189 0 1.43 CISPEP 4 ILE A 682 PRO A 683 0 -3.47 CRYST1 94.771 96.954 178.060 90.00 90.00 90.00 C 2 2 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 0.010552 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005616 0.00000