HEADER OXIDOREDUCTASE 06-MAY-20 6YYX
TITLE ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE (ASPH) OXYGENASE AND TPR DOMAINS
TITLE 2 IN COMPLEX WITH MANGANESE, 3-METHYL-2-OXOGLUTARATE, AND FACTOR X
TITLE 3 SUBSTRATE PEPTIDE FRAGMENT(39MER-4SER)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ASPARTATE BETA-HYDROXYLASE,ASP BETA-HYDROXYLASE,PEPTIDE-
COMPND 5 ASPARTATE BETA-DIOXYGENASE;
COMPND 6 EC: 1.14.11.16;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: COAGULATION FACTOR X;
COMPND 10 CHAIN: B;
COMPND 11 SYNONYM: STUART FACTOR,STUART-PROWER FACTOR;
COMPND 12 EC: 3.4.21.6;
COMPND 13 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: ASPH, BAH;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 GENE: F10;
SOURCE 13 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 32630
KEYWDS ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE, DIOXYGENASE, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.NAKASHIMA,L.BREWITZ,C.J.SCHOFIELD
REVDAT 3 06-NOV-24 6YYX 1 REMARK
REVDAT 2 24-JAN-24 6YYX 1 REMARK
REVDAT 1 17-MAR-21 6YYX 0
JRNL AUTH L.BREWITZ,Y.NAKASHIMA,C.J.SCHOFIELD
JRNL TITL SYNTHESIS OF 2-OXOGLUTARATE DERIVATIVES AND THEIR EVALUATION
JRNL TITL 2 AS COSUBSTRATES AND INHIBITORS OF HUMAN
JRNL TITL 3 ASPARTATE/ASPARAGINE-BETA-HYDROXYLASE
JRNL REF CHEM SCI V. 12 1327 2021
JRNL REFN ESSN 2041-6539
JRNL DOI 10.1039/D0SC04301J
REMARK 2
REMARK 2 RESOLUTION. 1.53 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.17.1_3660
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.21
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 59.9
REMARK 3 NUMBER OF REFLECTIONS : 48587
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.164
REMARK 3 R VALUE (WORKING SET) : 0.162
REMARK 3 FREE R VALUE : 0.192
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090
REMARK 3 FREE R VALUE TEST SET COUNT : 2474
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 50.2100 - 4.0200 0.98 4472 243 0.1300 0.1608
REMARK 3 2 4.0200 - 3.1900 0.99 4336 243 0.1272 0.1584
REMARK 3 3 3.1900 - 2.7900 0.98 4208 212 0.1632 0.1896
REMARK 3 4 2.7900 - 2.5300 0.94 4088 197 0.1734 0.2289
REMARK 3 5 2.5300 - 2.3500 0.88 3740 227 0.1806 0.2144
REMARK 3 6 2.3500 - 2.2100 0.85 3628 207 0.1885 0.2077
REMARK 3 7 2.2100 - 2.1000 0.81 3463 186 0.1952 0.2104
REMARK 3 8 2.1000 - 2.0100 0.77 3204 207 0.2061 0.2444
REMARK 3 9 2.0100 - 1.9300 0.72 3057 157 0.2279 0.2337
REMARK 3 10 1.9300 - 1.8700 0.65 2757 145 0.2316 0.2638
REMARK 3 11 1.8700 - 1.8100 0.59 2492 134 0.2511 0.2888
REMARK 3 12 1.8100 - 1.7600 0.53 2253 112 0.2610 0.2896
REMARK 3 13 1.7600 - 1.7100 0.45 1924 87 0.2673 0.3033
REMARK 3 14 1.7100 - 1.6700 0.32 1360 73 0.2784 0.2609
REMARK 3 15 1.6700 - 1.6300 0.16 706 27 0.3071 0.3758
REMARK 3 16 1.6300 - 1.6000 0.07 300 14 0.2883 0.3156
REMARK 3 17 1.6000 - 1.5600 0.02 100 2 0.2829 0.3491
REMARK 3 18 1.5600 - 1.5300 0.01 25 1 0.3299 0.7745
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.141
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.449
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 24.55
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.61
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.012 3671
REMARK 3 ANGLE : 1.281 4968
REMARK 3 CHIRALITY : 0.059 524
REMARK 3 PLANARITY : 0.008 648
REMARK 3 DIHEDRAL : 21.651 1365
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6YYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-20.
REMARK 100 THE DEPOSITION ID IS D_1292107206.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-JAN-20
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 : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : STARANISO
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48664
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530
REMARK 200 RESOLUTION RANGE LOW (A) : 86.590
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7
REMARK 200 DATA REDUNDANCY : 11.00
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 1.28900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 5JTC
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.67
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM BIS TRIS PROPANE, 200 MM
REMARK 280 SODIUM/POTASSIUM PHOSPHATE, 20% W/V PEG 3350, 1 MM MANGANESE
REMARK 280 CHLORIDE, 2 MM 3-METHYL-2-OXOGLUTARATE, 18 MG/ML PROTEIN, PH 6.5,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
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 25.11000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.63250
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.29550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.63250
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.11000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.29550
REMARK 290 SMTRY3 4 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: 2490 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19520 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 B 86
REMARK 465 GLY B 87
REMARK 465 ASP B 88
REMARK 465 GLN B 89
REMARK 465 SER B 90
REMARK 465 GLU B 91
REMARK 465 THR B 92
REMARK 465 SER B 93
REMARK 465 PRO B 94
REMARK 465 SER B 95
REMARK 465 GLN B 96
REMARK 465 ASN B 97
REMARK 465 GLN B 98
REMARK 465 GLU B 117
REMARK 465 GLY B 118
REMARK 465 LYS B 119
REMARK 465 ASN B 120
REMARK 465 SER B 121
REMARK 465 GLU B 122
REMARK 465 LEU B 123
REMARK 465 PHE B 124
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 LYS A 330 NZ
REMARK 470 LYS A 332 CE NZ
REMARK 470 LYS A 350 CD CE NZ
REMARK 470 LYS A 353 CE NZ
REMARK 470 LYS A 356 NZ
REMARK 470 ARG A 393 CZ NH1 NH2
REMARK 470 ARG A 437 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 448 CD OE1 NE2
REMARK 470 LYS A 475 NZ
REMARK 470 GLU A 479 CG CD OE1 OE2
REMARK 470 LYS A 541 CG CD CE NZ
REMARK 470 LYS A 545 CE NZ
REMARK 470 GLU A 548 CG CD OE1 OE2
REMARK 470 LEU A 549 CD1 CD2
REMARK 470 LYS A 552 CG CD CE NZ
REMARK 470 LYS A 571 NZ
REMARK 470 LYS A 579 CD CE NZ
REMARK 470 LYS A 609 CE NZ
REMARK 470 ARG A 635 CZ NH1 NH2
REMARK 470 LYS A 697 CD CE NZ
REMARK 470 GLU A 698 OE1 OE2
REMARK 470 ARG A 753 CD NE CZ NH1 NH2
REMARK 470 LEU B 113 CG CD1 CD2
REMARK 470 GLU B 114 CG CD OE1 OE2
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 O HOH A 937 O HOH A 1067 1.70
REMARK 500 O HOH A 1057 O HOH A 1097 1.80
REMARK 500 O HOH A 1151 O HOH A 1284 1.85
REMARK 500 O HOH A 1232 O HOH A 1279 1.88
REMARK 500 O HOH A 947 O HOH A 1123 1.88
REMARK 500 O HOH A 1135 O HOH A 1241 1.92
REMARK 500 O HOH A 1145 O HOH A 1258 1.92
REMARK 500 O HOH A 1236 O HOH A 1267 1.92
REMARK 500 O HOH A 927 O HOH A 1232 1.98
REMARK 500 O HOH A 916 O HOH A 1297 1.99
REMARK 500 O HOH B 214 O HOH B 215 2.00
REMARK 500 O HOH A 977 O HOH A 1286 2.02
REMARK 500 O HOH A 1247 O HOH A 1329 2.03
REMARK 500 O HOH A 1284 O HOH A 1306 2.04
REMARK 500 O HOH A 978 O HOH A 1267 2.05
REMARK 500 O HOH A 1095 O HOH A 1241 2.06
REMARK 500 O HOH A 947 O HOH A 1318 2.07
REMARK 500 O HOH A 1117 O HOH A 1175 2.09
REMARK 500 O HOH A 993 O HOH A 1214 2.10
REMARK 500 O HOH A 1258 O HOH A 1320 2.10
REMARK 500 O HOH A 1285 O HOH A 1291 2.10
REMARK 500 O HOH A 1132 O HOH A 1190 2.11
REMARK 500 O HOH A 1079 O HOH A 1302 2.13
REMARK 500 O HOH A 907 O HOH A 1186 2.14
REMARK 500 O HOH A 1233 O HOH B 214 2.15
REMARK 500 O HOH A 1160 O HOH A 1165 2.15
REMARK 500 O HOH A 1187 O HOH A 1335 2.18
REMARK 500 O HOH A 1026 O HOH A 1122 2.18
REMARK 500 O HOH A 966 O HOH A 1253 2.19
REMARK 500 O HOH A 1213 O HOH A 1331 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 1347 O HOH A 1351 4546 2.00
REMARK 500 O HOH A 1063 O HOH A 1153 4446 2.19
REMARK 500 O HOH A 1357 O HOH A 1358 3555 2.19
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 LEU A 717 CB - CG - CD1 ANGL. DEV. = -11.1 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 ARG A 393 62.27 37.75
REMARK 500 TYR A 583 46.90 -93.62
REMARK 500 ALA A 608 51.52 -145.94
REMARK 500 ASP A 616 40.65 -140.91
REMARK 500 ALA A 705 -122.67 50.05
REMARK 500 LYS B 102 -63.60 -93.93
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A1354 DISTANCE = 6.07 ANGSTROMS
REMARK 525 HOH A1355 DISTANCE = 6.07 ANGSTROMS
REMARK 525 HOH A1356 DISTANCE = 6.11 ANGSTROMS
REMARK 525 HOH A1357 DISTANCE = 7.49 ANGSTROMS
REMARK 525 HOH A1358 DISTANCE = 8.06 ANGSTROMS
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 MN A 801 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 679 NE2
REMARK 620 2 HIS A 725 NE2 85.8
REMARK 620 3 Q1Z A 802 O01 86.4 101.5
REMARK 620 4 Q1Z A 802 O02 162.3 96.4 75.9
REMARK 620 5 ASP B 103 OD2 102.8 171.0 81.8 76.2
REMARK 620 6 HOH B 205 O 98.2 91.7 166.3 99.3 84.6
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue Q1Z A 802
DBREF 6YYX A 330 758 UNP Q12797 ASPH_HUMAN 330 758
DBREF 6YYX B 86 124 UNP P00742 FA10_HUMAN 86 124
SEQADV 6YYX SER B 90 UNP P00742 CYS 90 ENGINEERED MUTATION
SEQADV 6YYX SER B 95 UNP P00742 CYS 95 ENGINEERED MUTATION
SEQADV 6YYX SER B 112 UNP P00742 CYS 112 ENGINEERED MUTATION
SEQADV 6YYX SER B 121 UNP P00742 CYS 121 ENGINEERED MUTATION
SEQRES 1 A 429 LYS PRO LYS LEU LEU ASN LYS PHE ASP LYS THR ILE LYS
SEQRES 2 A 429 ALA GLU LEU ASP ALA ALA GLU LYS LEU ARG LYS ARG GLY
SEQRES 3 A 429 LYS ILE GLU GLU ALA VAL ASN ALA PHE LYS GLU LEU VAL
SEQRES 4 A 429 ARG LYS TYR PRO GLN SER PRO ARG ALA ARG TYR GLY LYS
SEQRES 5 A 429 ALA GLN CYS GLU ASP ASP LEU ALA GLU LYS ARG ARG SER
SEQRES 6 A 429 ASN GLU VAL LEU ARG GLY ALA ILE GLU THR TYR GLN GLU
SEQRES 7 A 429 VAL ALA SER LEU PRO ASP VAL PRO ALA ASP LEU LEU LYS
SEQRES 8 A 429 LEU SER LEU LYS ARG ARG SER ASP ARG GLN GLN PHE LEU
SEQRES 9 A 429 GLY HIS MET ARG GLY SER LEU LEU THR LEU GLN ARG LEU
SEQRES 10 A 429 VAL GLN LEU PHE PRO ASN ASP THR SER LEU LYS ASN ASP
SEQRES 11 A 429 LEU GLY VAL GLY TYR LEU LEU ILE GLY ASP ASN ASP ASN
SEQRES 12 A 429 ALA LYS LYS VAL TYR GLU GLU VAL LEU SER VAL THR PRO
SEQRES 13 A 429 ASN ASP GLY PHE ALA LYS VAL HIS TYR GLY PHE ILE LEU
SEQRES 14 A 429 LYS ALA GLN ASN LYS ILE ALA GLU SER ILE PRO TYR LEU
SEQRES 15 A 429 LYS GLU GLY ILE GLU SER GLY ASP PRO GLY THR ASP ASP
SEQRES 16 A 429 GLY ARG PHE TYR PHE HIS LEU GLY ASP ALA MET GLN ARG
SEQRES 17 A 429 VAL GLY ASN LYS GLU ALA TYR LYS TRP TYR GLU LEU GLY
SEQRES 18 A 429 HIS LYS ARG GLY HIS PHE ALA SER VAL TRP GLN ARG SER
SEQRES 19 A 429 LEU TYR ASN VAL ASN GLY LEU LYS ALA GLN PRO TRP TRP
SEQRES 20 A 429 THR PRO LYS GLU THR GLY TYR THR GLU LEU VAL LYS SER
SEQRES 21 A 429 LEU GLU ARG ASN TRP LYS LEU ILE ARG ASP GLU GLY LEU
SEQRES 22 A 429 ALA VAL MET ASP LYS ALA LYS GLY LEU PHE LEU PRO GLU
SEQRES 23 A 429 ASP GLU ASN LEU ARG GLU LYS GLY ASP TRP SER GLN PHE
SEQRES 24 A 429 THR LEU TRP GLN GLN GLY ARG ARG ASN GLU ASN ALA CYS
SEQRES 25 A 429 LYS GLY ALA PRO LYS THR CYS THR LEU LEU GLU LYS PHE
SEQRES 26 A 429 PRO GLU THR THR GLY CYS ARG ARG GLY GLN ILE LYS TYR
SEQRES 27 A 429 SER ILE MET HIS PRO GLY THR HIS VAL TRP PRO HIS THR
SEQRES 28 A 429 GLY PRO THR ASN CYS ARG LEU ARG MET HIS LEU GLY LEU
SEQRES 29 A 429 VAL ILE PRO LYS GLU GLY CYS LYS ILE ARG CYS ALA ASN
SEQRES 30 A 429 GLU THR LYS THR TRP GLU GLU GLY LYS VAL LEU ILE PHE
SEQRES 31 A 429 ASP ASP SER PHE GLU HIS GLU VAL TRP GLN ASP ALA SER
SEQRES 32 A 429 SER PHE ARG LEU ILE PHE ILE VAL ASP VAL TRP HIS PRO
SEQRES 33 A 429 GLU LEU THR PRO GLN GLN ARG ARG SER LEU PRO ALA ILE
SEQRES 1 B 39 ASP GLY ASP GLN SER GLU THR SER PRO SER GLN ASN GLN
SEQRES 2 B 39 GLY LYS CYS LYS ASP GLY LEU GLY GLU TYR THR CYS THR
SEQRES 3 B 39 SER LEU GLU GLY PHE GLU GLY LYS ASN SER GLU LEU PHE
HET MN A 801 1
HET Q1Z A 802 17
HETNAM MN MANGANESE (II) ION
HETNAM Q1Z (3~{R})-3-METHYL-2-OXIDANYLIDENE-PENTANEDIOIC ACID
FORMUL 3 MN MN 2+
FORMUL 4 Q1Z C6 H8 O5
FORMUL 5 HOH *474(H2 O)
HELIX 1 AA1 ASN A 335 ILE A 341 1 7
HELIX 2 AA2 ILE A 341 ARG A 354 1 14
HELIX 3 AA3 LYS A 356 TYR A 371 1 16
HELIX 4 AA4 SER A 374 ARG A 393 1 20
HELIX 5 AA5 SER A 394 LEU A 411 1 18
HELIX 6 AA6 PRO A 415 LEU A 433 1 19
HELIX 7 AA7 HIS A 435 PHE A 450 1 16
HELIX 8 AA8 ASP A 453 ILE A 467 1 15
HELIX 9 AA9 ASP A 469 THR A 484 1 16
HELIX 10 AB1 ASP A 487 GLN A 501 1 15
HELIX 11 AB2 LYS A 503 SER A 517 1 15
HELIX 12 AB3 ASP A 524 GLY A 539 1 16
HELIX 13 AB4 GLU A 542 ARG A 553 1 12
HELIX 14 AB5 THR A 577 GLY A 582 1 6
HELIX 15 AB6 TYR A 583 ASN A 593 1 11
HELIX 16 AB7 ASN A 593 ALA A 608 1 16
HELIX 17 AB8 LYS A 609 PHE A 612 5 4
HELIX 18 AB9 ASN A 637 ALA A 644 1 8
HELIX 19 AC1 ALA A 644 GLU A 652 1 9
HELIX 20 AC2 PHE A 654 GLY A 659 1 6
HELIX 21 AC3 THR A 748 LEU A 755 1 8
SHEET 1 AA1 7 TRP A 575 TRP A 576 0
SHEET 2 AA1 7 VAL A 716 PHE A 719 -1 O ILE A 718 N TRP A 576
SHEET 3 AA1 7 ARG A 686 VAL A 694 -1 N ARG A 688 O PHE A 719
SHEET 4 AA1 7 ARG A 735 TRP A 743 -1 O PHE A 738 N LEU A 691
SHEET 5 AA1 7 GLN A 664 MET A 670 -1 N LYS A 666 O ILE A 739
SHEET 6 AA1 7 TRP A 625 GLN A 632 -1 N LEU A 630 O ILE A 665
SHEET 7 AA1 7 LEU A 613 PRO A 614 -1 N LEU A 613 O GLN A 627
SHEET 1 AA2 7 TRP A 575 TRP A 576 0
SHEET 2 AA2 7 VAL A 716 PHE A 719 -1 O ILE A 718 N TRP A 576
SHEET 3 AA2 7 ARG A 686 VAL A 694 -1 N ARG A 688 O PHE A 719
SHEET 4 AA2 7 ARG A 735 TRP A 743 -1 O PHE A 738 N LEU A 691
SHEET 5 AA2 7 GLN A 664 MET A 670 -1 N LYS A 666 O ILE A 739
SHEET 6 AA2 7 TRP A 625 GLN A 632 -1 N LEU A 630 O ILE A 665
SHEET 7 AA2 7 ARG A 635 ARG A 636 -1 O ARG A 635 N GLN A 632
SHEET 1 AA3 5 ARG A 620 LYS A 622 0
SHEET 2 AA3 5 THR A 674 HIS A 679 -1 O HIS A 675 N GLU A 621
SHEET 3 AA3 5 HIS A 725 GLN A 729 -1 O VAL A 727 N VAL A 676
SHEET 4 AA3 5 CYS A 700 CYS A 704 -1 N ARG A 703 O GLU A 726
SHEET 5 AA3 5 GLU A 707 LYS A 709 -1 O LYS A 709 N ILE A 702
SSBOND 1 CYS A 641 CYS A 648 1555 1555 2.09
SSBOND 2 CYS B 101 CYS B 110 1555 1555 2.12
LINK NE2 HIS A 679 MN MN A 801 1555 1555 2.22
LINK NE2 HIS A 725 MN MN A 801 1555 1555 2.18
LINK MN MN A 801 O01 Q1Z A 802 1555 1555 2.10
LINK MN MN A 801 O02 Q1Z A 802 1555 1555 2.14
LINK MN MN A 801 OD2 ASP B 103 1555 1555 2.68
LINK MN MN A 801 O HOH B 205 1555 1555 2.11
SITE 1 AC1 5 HIS A 679 HIS A 725 Q1Z A 802 ASP B 103
SITE 2 AC1 5 HOH B 205
SITE 1 AC2 13 TRP A 625 SER A 668 HIS A 679 ARG A 688
SITE 2 AC2 13 HIS A 690 TRP A 711 HIS A 725 VAL A 727
SITE 3 AC2 13 ARG A 735 ILE A 737 ILE A 739 MN A 801
SITE 4 AC2 13 ASP B 103
CRYST1 50.220 86.591 123.265 90.00 90.00 90.00 P 21 21 21 4
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 0.019912 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011549 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008113 0.00000