HEADER OXIDOREDUCTASE 29-JUN-22 7YBC TITLE ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE (ASPH) OXYGENASE AND TPR DOMAINS TITLE 2 IN COMPLEX WITH (S)-4-HYDROXY-4-METHYL-2-OXOGLUTARATE AND FACTOR X- TITLE 3 DERIVED PEPTIDE (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; COMPND 14 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: ASPH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 GENE: F10; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE, DIOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKASHIMA,L.BREWITZ,C.J.SCHOFIELD REVDAT 2 29-NOV-23 7YBC 1 REMARK REVDAT 1 05-JUL-23 7YBC 0 JRNL AUTH Y.NAKASHIMA,L.BREWITZ,C.J.SCHOFIELD JRNL TITL ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE (ASPH) OXYGENASE AND JRNL TITL 2 TPR DOMAINS IN COMPLEX WITH JRNL TITL 3 (S)-4-HYDROXY-4-METHYL-2-OXOGLUTARATE AND FACTOR X-DERIVED JRNL TITL 4 PEPTIDE (39MER-4SER) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 48357 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 2324 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 43.6000 - 4.7300 1.00 2927 137 0.1854 0.1945 REMARK 3 2 4.7300 - 3.7500 1.00 2779 146 0.1336 0.1393 REMARK 3 3 3.7500 - 3.2800 1.00 2757 123 0.1548 0.1486 REMARK 3 4 3.2800 - 2.9800 1.00 2718 140 0.1734 0.2052 REMARK 3 5 2.9800 - 2.7600 1.00 2718 146 0.1716 0.2076 REMARK 3 6 2.7600 - 2.6000 1.00 2704 148 0.1748 0.2338 REMARK 3 7 2.6000 - 2.4700 1.00 2697 135 0.1676 0.1923 REMARK 3 8 2.4700 - 2.3600 1.00 2691 143 0.1744 0.2445 REMARK 3 9 2.3600 - 2.2700 1.00 2704 111 0.1746 0.2022 REMARK 3 10 2.2700 - 2.1900 1.00 2676 123 0.1815 0.2406 REMARK 3 11 2.1900 - 2.1300 1.00 2715 126 0.1807 0.1951 REMARK 3 12 2.1300 - 2.0600 1.00 2691 135 0.2125 0.2258 REMARK 3 13 2.0600 - 2.0100 1.00 2662 127 0.2228 0.2732 REMARK 3 14 2.0100 - 1.9600 1.00 2703 119 0.2423 0.2919 REMARK 3 15 1.9600 - 1.9200 1.00 2635 164 0.2660 0.2987 REMARK 3 16 1.9200 - 1.8800 0.99 2630 148 0.2964 0.3041 REMARK 3 17 1.8800 - 1.8400 0.99 2626 153 0.3227 0.3393 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.219 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.551 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.06 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 : 0.005 3713 REMARK 3 ANGLE : 0.786 5026 REMARK 3 CHIRALITY : 0.045 528 REMARK 3 PLANARITY : 0.005 659 REMARK 3 DIHEDRAL : 20.257 1394 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 538 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.4226 -13.8938 12.1515 REMARK 3 T TENSOR REMARK 3 T11: 0.3089 T22: 0.2802 REMARK 3 T33: 0.2507 T12: -0.0765 REMARK 3 T13: -0.0266 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.4679 L22: 1.3126 REMARK 3 L33: 1.3981 L12: -0.1530 REMARK 3 L13: -0.4791 L23: -1.1727 REMARK 3 S TENSOR REMARK 3 S11: 0.1898 S12: -0.0165 S13: 0.0922 REMARK 3 S21: -0.0789 S22: -0.0340 S23: 0.0017 REMARK 3 S31: 0.0654 S32: -0.1630 S33: 0.0022 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 539 THROUGH 758 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9893 -25.6088 45.7667 REMARK 3 T TENSOR REMARK 3 T11: 0.1996 T22: 0.2168 REMARK 3 T33: 0.2155 T12: -0.0035 REMARK 3 T13: 0.0044 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 1.3822 L22: 0.7545 REMARK 3 L33: 1.1580 L12: 0.3278 REMARK 3 L13: 0.8599 L23: 0.1602 REMARK 3 S TENSOR REMARK 3 S11: -0.0376 S12: 0.2534 S13: -0.0180 REMARK 3 S21: -0.1061 S22: 0.0887 S23: -0.0161 REMARK 3 S31: 0.0377 S32: 0.1698 S33: 0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 99 THROUGH 103 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4741 -18.7899 38.5763 REMARK 3 T TENSOR REMARK 3 T11: 0.3653 T22: 0.6546 REMARK 3 T33: 0.3466 T12: 0.0222 REMARK 3 T13: -0.0383 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.0072 L22: 0.0335 REMARK 3 L33: 0.0047 L12: -0.0119 REMARK 3 L13: 0.0063 L23: -0.0138 REMARK 3 S TENSOR REMARK 3 S11: 0.1729 S12: 0.0766 S13: 0.0769 REMARK 3 S21: -0.0627 S22: -0.0981 S23: 0.0367 REMARK 3 S31: -0.0784 S32: -0.0508 S33: -0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 104 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6274 -21.7662 31.5899 REMARK 3 T TENSOR REMARK 3 T11: 0.3757 T22: 0.4770 REMARK 3 T33: 0.3134 T12: -0.0679 REMARK 3 T13: -0.0370 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.0056 L22: 0.0103 REMARK 3 L33: 0.0122 L12: 0.0048 REMARK 3 L13: 0.0001 L23: -0.0118 REMARK 3 S TENSOR REMARK 3 S11: 0.0749 S12: 0.0359 S13: 0.1308 REMARK 3 S21: -0.1123 S22: -0.0129 S23: 0.0489 REMARK 3 S31: -0.0983 S32: -0.1906 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 109 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6467 -15.8479 28.1199 REMARK 3 T TENSOR REMARK 3 T11: 0.4994 T22: 0.6274 REMARK 3 T33: 0.3123 T12: -0.1287 REMARK 3 T13: -0.0556 T23: 0.0758 REMARK 3 L TENSOR REMARK 3 L11: 0.0203 L22: 0.0240 REMARK 3 L33: 0.0134 L12: 0.0124 REMARK 3 L13: -0.0099 L23: -0.0061 REMARK 3 S TENSOR REMARK 3 S11: -0.3422 S12: 0.0247 S13: -0.0196 REMARK 3 S21: -0.1688 S22: -0.2624 S23: 0.1433 REMARK 3 S31: -0.0850 S32: 0.0360 S33: -0.0002 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 114 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6275 -9.7976 20.1105 REMARK 3 T TENSOR REMARK 3 T11: 0.4654 T22: 0.7729 REMARK 3 T33: 0.5213 T12: -0.1874 REMARK 3 T13: -0.1312 T23: 0.1868 REMARK 3 L TENSOR REMARK 3 L11: 0.1145 L22: 0.0023 REMARK 3 L33: 0.6954 L12: -0.0116 REMARK 3 L13: -0.2479 L23: 0.0430 REMARK 3 S TENSOR REMARK 3 S11: 0.0525 S12: 0.0017 S13: 0.0253 REMARK 3 S21: 0.0738 S22: -0.0204 S23: -0.1215 REMARK 3 S31: 0.0231 S32: 0.0465 S33: 0.0000 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 7YBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99990 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 71.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.27900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 4.17600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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 (%): 51.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 20 % REMARK 280 W/V POLYETHYLENE GLYCOL 3,350, 0.1 M BIS TRIS PROPANE, PH 8.5, 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 25.18600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.19800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.52450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.19800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.18600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.52450 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: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 CG CD CE NZ REMARK 470 LYS A 332 CE NZ REMARK 470 LYS A 353 CE NZ REMARK 470 LYS A 356 CE NZ REMARK 470 GLU A 358 CD OE1 OE2 REMARK 470 GLU A 366 CD OE1 OE2 REMARK 470 GLN A 448 CD OE1 NE2 REMARK 470 LYS A 541 CG CD CE NZ REMARK 470 LYS A 545 CE NZ REMARK 470 LYS A 552 CD CE NZ REMARK 470 LYS A 571 NZ REMARK 470 LYS A 579 CD CE NZ REMARK 470 ARG A 635 CZ NH1 NH2 REMARK 470 LYS A 697 CD CE NZ REMARK 470 GLU A 698 CD OE1 OE2 REMARK 470 ARG A 753 CD NE CZ NH1 NH2 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 1051 O HOH A 1087 1.95 REMARK 500 O HOH A 968 O HOH A 1115 1.95 REMARK 500 O HOH A 926 O HOH A 1087 1.99 REMARK 500 O HOH A 1104 O HOH A 1180 2.07 REMARK 500 O HOH A 1117 O HOH A 1134 2.07 REMARK 500 O HOH A 1054 O HOH A 1083 2.10 REMARK 500 O HOH A 1110 O HOH A 1130 2.13 REMARK 500 O HOH A 1038 O HOH A 1103 2.16 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 1058 O HOH A 1104 4546 1.98 REMARK 500 O HOH A 1058 O HOH A 1180 4546 2.03 REMARK 500 O HOH A 986 O HOH A 1134 4446 2.11 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 TYR A 583 49.79 -91.76 REMARK 500 ALA A 608 49.26 -148.87 REMARK 500 ALA A 705 -128.04 62.86 REMARK 500 LYS B 102 -65.55 -97.78 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 A1197 DISTANCE = 6.02 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 83.5 REMARK 620 3 IOW A 803 O01 176.3 98.6 REMARK 620 4 IOW A 803 O03 100.0 102.3 76.6 REMARK 620 N 1 2 3 DBREF 7YBC A 330 758 UNP Q12797 ASPH_HUMAN 330 758 DBREF 7YBC B 86 124 UNP P00742 FA10_HUMAN 86 124 SEQADV 7YBC SER B 90 UNP P00742 CYS 90 ENGINEERED MUTATION SEQADV 7YBC SER B 95 UNP P00742 CYS 95 ENGINEERED MUTATION SEQADV 7YBC SER B 112 UNP P00742 CYS 112 ENGINEERED MUTATION SEQADV 7YBC 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 GOL A 802 14 HET IOW A 803 18 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM IOW (2~{S})-2-METHYL-2-OXIDANYL-4-OXIDANYLIDENE- HETNAM 2 IOW PENTANEDIOIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN MN 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 IOW C6 H8 O6 FORMUL 6 HOH *310(H2 O) HELIX 1 AA1 ASN A 335 ILE A 341 1 7 HELIX 2 AA2 ILE A 341 GLY A 355 1 15 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 GLY A 518 1 16 HELIX 12 AB3 ASP A 524 VAL A 538 1 15 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 HIS A 690 O LEU A 717 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 HIS A 690 O LEU A 717 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 2.04 SSBOND 2 CYS B 101 CYS B 110 1555 1555 2.04 LINK NE2 HIS A 679 MN MN A 801 1555 1555 2.29 LINK NE2 HIS A 725 MN MN A 801 1555 1555 2.24 LINK MN MN A 801 O01 IOW A 803 1555 1555 2.18 LINK MN MN A 801 O03 IOW A 803 1555 1555 2.26 CRYST1 50.372 87.049 124.396 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 0.019852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008039 0.00000