HEADER OXIDOREDUCTASE 29-JUN-22 7YB8 TITLE ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE (ASPH) OXYGENASE AND TPR DOMAINS TITLE 2 IN COMPLEX WITH D-2-HYDROXYGLUTARATE AND FACTOR X-DERIVED PEPTIDE TITLE 3 (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 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; 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 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS ASPARTYL/ASPARAGINYL BETA-HYDROXYLASE, DIOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKASHIMA,L.BREWITZ,C.J.SCHOFIELD REVDAT 2 29-NOV-23 7YB8 1 REMARK REVDAT 1 05-JUL-23 7YB8 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 D-2-HYDROXYGLUTARATE AND FACTOR JRNL TITL 3 X-DERIVED PEPTIDE (39MER-4SER) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 69097 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3494 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 50.7800 - 5.7900 1.00 2844 157 0.1736 0.2217 REMARK 3 2 5.7900 - 4.5900 1.00 2842 152 0.1587 0.1825 REMARK 3 3 4.5900 - 4.0100 1.00 2847 150 0.1513 0.2070 REMARK 3 4 4.0100 - 3.6500 1.00 2833 152 0.1614 0.1652 REMARK 3 5 3.6500 - 3.3900 1.00 2864 151 0.1838 0.1990 REMARK 3 6 3.3900 - 3.1900 1.00 2864 147 0.2107 0.2514 REMARK 3 7 3.1900 - 3.0300 1.00 2827 158 0.2218 0.2604 REMARK 3 8 3.0300 - 2.8900 1.00 2861 152 0.2299 0.2632 REMARK 3 9 2.8900 - 2.7800 1.00 2826 150 0.2621 0.2467 REMARK 3 10 2.7800 - 2.6900 1.00 2878 151 0.2541 0.2578 REMARK 3 11 2.6900 - 2.6000 1.00 2808 154 0.2569 0.2803 REMARK 3 12 2.6000 - 2.5300 1.00 2866 150 0.2693 0.2594 REMARK 3 13 2.5300 - 2.4600 1.00 2799 151 0.2636 0.2970 REMARK 3 14 2.4600 - 2.4000 1.00 2873 152 0.2868 0.3131 REMARK 3 15 2.4000 - 2.3500 1.00 2839 151 0.3009 0.3825 REMARK 3 16 2.3500 - 2.3000 0.99 2827 153 0.3198 0.3663 REMARK 3 17 2.3000 - 2.2500 0.98 2737 148 0.3416 0.3155 REMARK 3 18 2.2500 - 2.2100 0.98 2840 150 0.3462 0.4044 REMARK 3 19 2.2100 - 2.1700 0.95 2666 139 0.3519 0.3545 REMARK 3 20 2.1700 - 2.1300 0.95 2762 142 0.3616 0.3663 REMARK 3 21 2.1300 - 2.1000 0.88 2525 132 0.3724 0.3998 REMARK 3 22 2.1000 - 2.0700 0.83 2335 131 0.3815 0.3809 REMARK 3 23 2.0700 - 2.0400 0.71 2032 99 0.4037 0.4067 REMARK 3 24 2.0400 - 2.0100 0.49 1393 77 0.4020 0.4343 REMARK 3 25 2.0100 - 1.9800 0.29 815 45 0.4181 0.4944 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) : 0.356 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.63 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 : 0.002 3714 REMARK 3 ANGLE : 0.500 5017 REMARK 3 CHIRALITY : 0.038 525 REMARK 3 PLANARITY : 0.003 656 REMARK 3 DIHEDRAL : 19.617 1406 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 537 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.1070 32.0777 50.0668 REMARK 3 T TENSOR REMARK 3 T11: 0.4763 T22: 0.3491 REMARK 3 T33: 0.4255 T12: 0.0823 REMARK 3 T13: -0.0712 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.1022 L22: 1.1504 REMARK 3 L33: 1.9983 L12: 0.1912 REMARK 3 L13: -0.5624 L23: 1.7184 REMARK 3 S TENSOR REMARK 3 S11: 0.2354 S12: 0.0565 S13: -0.0273 REMARK 3 S21: 0.0152 S22: -0.0994 S23: 0.0421 REMARK 3 S31: 0.0359 S32: -0.0788 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 538 THROUGH 758 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.3672 19.2948 16.4718 REMARK 3 T TENSOR REMARK 3 T11: 0.2784 T22: 0.3488 REMARK 3 T33: 0.2894 T12: -0.0607 REMARK 3 T13: -0.0104 T23: 0.0331 REMARK 3 L TENSOR REMARK 3 L11: 1.2915 L22: 0.5461 REMARK 3 L33: 2.6604 L12: -0.1132 REMARK 3 L13: 1.5677 L23: 0.0641 REMARK 3 S TENSOR REMARK 3 S11: 0.0806 S12: -0.2658 S13: -0.0701 REMARK 3 S21: 0.0822 S22: 0.0551 S23: -0.0250 REMARK 3 S31: 0.2121 S32: -0.5173 S33: 0.0052 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 99 THROUGH 103 ) REMARK 3 ORIGIN FOR THE GROUP (A): 59.9555 26.3150 23.5184 REMARK 3 T TENSOR REMARK 3 T11: 0.4043 T22: 0.4081 REMARK 3 T33: 0.4005 T12: -0.0340 REMARK 3 T13: 0.0412 T23: -0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.0118 L22: 0.0257 REMARK 3 L33: 0.0098 L12: -0.0072 REMARK 3 L13: -0.0121 L23: 0.0087 REMARK 3 S TENSOR REMARK 3 S11: 0.1306 S12: 0.1765 S13: -0.0114 REMARK 3 S21: -0.0319 S22: 0.0679 S23: 0.2786 REMARK 3 S31: -0.0027 S32: 0.0102 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 104 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): 63.7868 23.3683 30.6560 REMARK 3 T TENSOR REMARK 3 T11: 0.4342 T22: 0.4942 REMARK 3 T33: 0.5808 T12: 0.0826 REMARK 3 T13: -0.0894 T23: 0.0286 REMARK 3 L TENSOR REMARK 3 L11: 0.0069 L22: 0.0062 REMARK 3 L33: 0.0289 L12: -0.0058 REMARK 3 L13: 0.0117 L23: 0.0012 REMARK 3 S TENSOR REMARK 3 S11: 0.0534 S12: 0.0665 S13: 0.2372 REMARK 3 S21: 0.1173 S22: 0.0191 S23: -0.2121 REMARK 3 S31: -0.1522 S32: 0.1545 S33: 0.0004 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 109 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.5576 29.3596 33.8930 REMARK 3 T TENSOR REMARK 3 T11: 0.7001 T22: 0.7851 REMARK 3 T33: 0.5102 T12: 0.1443 REMARK 3 T13: -0.0033 T23: -0.0857 REMARK 3 L TENSOR REMARK 3 L11: 0.0161 L22: 0.0305 REMARK 3 L33: 0.0321 L12: -0.0221 REMARK 3 L13: 0.0114 L23: 0.0064 REMARK 3 S TENSOR REMARK 3 S11: -0.1290 S12: -0.3551 S13: 0.2216 REMARK 3 S21: 0.6304 S22: 0.0951 S23: 0.1452 REMARK 3 S31: -0.0780 S32: -0.2018 S33: 0.0006 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 114 THROUGH 116 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.9499 34.6444 42.4584 REMARK 3 T TENSOR REMARK 3 T11: 0.9878 T22: 0.9602 REMARK 3 T33: 0.8318 T12: 0.2234 REMARK 3 T13: 0.2572 T23: -0.2132 REMARK 3 L TENSOR REMARK 3 L11: 0.1175 L22: 0.0051 REMARK 3 L33: 0.9096 L12: 0.0151 REMARK 3 L13: -0.2415 L23: -0.0630 REMARK 3 S TENSOR REMARK 3 S11: 0.1033 S12: -0.0067 S13: -0.0320 REMARK 3 S21: 0.1584 S22: -0.0839 S23: 0.0692 REMARK 3 S31: -0.0153 S32: 0.0403 S33: 0.0002 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 7YB8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.96857 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69097 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 91.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.23800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 3.52700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.300 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 (%): 52.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM CHLORIDE, 20 % W/V REMARK 280 POLYETHYLENE GLYCOL 6,000, 0.1 M TRIS-HCL, PH 8.0, VAPOR REMARK 280 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 24.93950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.17550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.53150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.17550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.93950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.53150 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: 3140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19620 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 NZ REMARK 470 LYS A 353 NZ REMARK 470 LYS A 356 CE NZ REMARK 470 LYS A 391 CD CE NZ REMARK 470 LYS A 541 CD CE NZ REMARK 470 LYS A 545 CG CD CE NZ REMARK 470 LYS A 552 CD CE NZ REMARK 470 LYS A 579 CD CE NZ REMARK 470 LYS A 609 CD CE NZ REMARK 470 LYS A 697 CE NZ REMARK 470 GLU B 114 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 1170 O HOH A 1173 2.04 REMARK 500 O HOH A 1191 O HOH A 1192 2.11 REMARK 500 O HOH A 1162 O HOH A 1182 2.17 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 LYS A 356 83.42 -68.39 REMARK 500 ASP A 469 76.46 -101.04 REMARK 500 TYR A 583 49.51 -93.75 REMARK 500 ALA A 608 58.54 -147.43 REMARK 500 ALA A 705 -115.22 62.86 REMARK 500 LYS B 102 -64.70 -104.08 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 MN A1003 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 679 NE2 REMARK 620 2 HIS A 725 NE2 80.9 REMARK 620 3 2HG A1004 O3 91.8 98.0 REMARK 620 4 2HG A1004 O2 165.8 111.9 80.6 REMARK 620 N 1 2 3 DBREF 7YB8 A 330 758 UNP Q12797 ASPH_HUMAN 330 758 DBREF 7YB8 B 86 124 PDB 7YB8 7YB8 86 124 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 GOL A1001 12 HET GOL A1002 14 HET MN A1003 1 HET 2HG A1004 16 HETNAM GOL GLYCEROL HETNAM MN MANGANESE (II) ION HETNAM 2HG (2R)-2-HYDROXYPENTANEDIOIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 MN MN 2+ FORMUL 6 2HG C5 H8 O5 FORMUL 7 HOH *119(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 GLY A 434 1 20 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 3 LEU A 613 PRO A 614 0 SHEET 2 AA1 3 TRP A 625 GLN A 632 -1 O GLN A 627 N LEU A 613 SHEET 3 AA1 3 ARG A 635 ARG A 636 -1 O ARG A 635 N GLN A 632 SHEET 1 AA2 6 LEU A 613 PRO A 614 0 SHEET 2 AA2 6 TRP A 625 GLN A 632 -1 O GLN A 627 N LEU A 613 SHEET 3 AA2 6 GLN A 664 MET A 670 -1 O ILE A 665 N LEU A 630 SHEET 4 AA2 6 ARG A 735 TRP A 743 -1 O ILE A 739 N LYS A 666 SHEET 5 AA2 6 ARG A 686 VAL A 694 -1 N LEU A 691 O PHE A 738 SHEET 6 AA2 6 VAL A 716 PHE A 719 -1 O LEU A 717 N HIS A 690 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 A1003 1555 1555 2.26 LINK NE2 HIS A 725 MN MN A1003 1555 1555 1.96 LINK MN MN A1003 O3 2HG A1004 1555 1555 1.96 LINK MN MN A1003 O2 2HG A1004 1555 1555 2.15 CRYST1 49.879 91.063 122.351 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 0.020049 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010981 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008173 0.00000