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 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 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