HEADER ISOMERASE 04-AUG-22 8DYL TITLE CRYSTAL STRUCTURE OF HUMAN METHYLMALONYL-COA MUTASE BOUND TO TITLE 2 AQUOCOBALAMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLMALONYL-COA MUTASE, MITOCHONDRIAL; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: MCM,METHYLMALONYL-COA ISOMERASE; COMPND 5 EC: 5.4.99.2; COMPND 6 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: MMUT, MUT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COBALAMIN, MUTASE, VITAMIN B12, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.N.MASCARENHAS,H.GOUDA,R.BANERJEE REVDAT 3 25-OCT-23 8DYL 1 REMARK REVDAT 2 23-AUG-23 8DYL 1 JRNL REVDAT 1 12-JUL-23 8DYL 0 JRNL AUTH H.GOUDA,R.MASCARENHAS,M.RUETZ,M.YAW,R.BANERJEE JRNL TITL BIVALENT MOLECULAR MIMICRY BY ADP PROTECTS METAL REDOX STATE JRNL TITL 2 AND PROMOTES COENZYME B 12 REPAIR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 77120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 36888659 JRNL DOI 10.1073/PNAS.2220677120 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 61384 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 3126 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 39.7630 - 5.3199 1.00 2864 173 0.1770 0.1770 REMARK 3 2 5.3199 - 4.2241 1.00 2808 144 0.1543 0.1675 REMARK 3 3 4.2241 - 3.6906 1.00 2747 143 0.1548 0.1967 REMARK 3 4 3.6906 - 3.3533 1.00 2732 162 0.1729 0.2113 REMARK 3 5 3.3533 - 3.1131 1.00 2713 155 0.1845 0.2079 REMARK 3 6 3.1131 - 2.9296 1.00 2725 156 0.1845 0.2406 REMARK 3 7 2.9296 - 2.7829 1.00 2721 134 0.1854 0.2265 REMARK 3 8 2.7829 - 2.6618 1.00 2699 138 0.1797 0.2523 REMARK 3 9 2.6618 - 2.5593 1.00 2703 135 0.1733 0.2353 REMARK 3 10 2.5593 - 2.4710 1.00 2713 128 0.1706 0.2043 REMARK 3 11 2.4710 - 2.3938 1.00 2697 170 0.1692 0.2078 REMARK 3 12 2.3938 - 2.3254 1.00 2710 141 0.1671 0.2216 REMARK 3 13 2.3254 - 2.2642 1.00 2684 155 0.1771 0.2250 REMARK 3 14 2.2642 - 2.2089 1.00 2687 144 0.1758 0.2323 REMARK 3 15 2.2089 - 2.1587 1.00 2695 134 0.1811 0.2216 REMARK 3 16 2.1587 - 2.1128 1.00 2654 173 0.1874 0.2301 REMARK 3 17 2.1128 - 2.0705 0.99 2674 142 0.1846 0.2308 REMARK 3 18 2.0705 - 2.0314 0.97 2621 124 0.1827 0.2385 REMARK 3 19 2.0314 - 1.9952 0.94 2505 142 0.1919 0.2651 REMARK 3 20 1.9952 - 1.9613 0.90 2400 130 0.2045 0.2424 REMARK 3 21 1.9613 - 1.9297 0.87 2366 107 0.2313 0.2732 REMARK 3 22 1.9297 - 1.9000 0.80 2140 96 0.2340 0.2608 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.64 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 36 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.4929 0.6181 7.0781 REMARK 3 T TENSOR REMARK 3 T11: 0.2087 T22: 0.3390 REMARK 3 T33: 0.3303 T12: -0.0024 REMARK 3 T13: -0.0591 T23: -0.1567 REMARK 3 L TENSOR REMARK 3 L11: 0.2460 L22: 1.5722 REMARK 3 L33: 1.6417 L12: -0.0224 REMARK 3 L13: -0.5111 L23: -0.0476 REMARK 3 S TENSOR REMARK 3 S11: 0.0894 S12: -0.0458 S13: 0.0283 REMARK 3 S21: 0.0118 S22: 0.1293 S23: -0.3336 REMARK 3 S31: -0.1108 S32: 0.3957 S33: -0.1987 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 116 THROUGH 252 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.0157 -26.0087 22.1343 REMARK 3 T TENSOR REMARK 3 T11: 0.2659 T22: 0.2137 REMARK 3 T33: 0.3563 T12: -0.0495 REMARK 3 T13: -0.0415 T23: -0.0661 REMARK 3 L TENSOR REMARK 3 L11: 2.0912 L22: 1.6472 REMARK 3 L33: 0.9525 L12: 0.4338 REMARK 3 L13: 0.2060 L23: 0.2698 REMARK 3 S TENSOR REMARK 3 S11: -0.0953 S12: 0.1499 S13: -0.5513 REMARK 3 S21: 0.0146 S22: 0.1317 S23: -0.1786 REMARK 3 S31: 0.0452 S32: 0.0252 S33: -0.0352 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 253 THROUGH 398 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.6054 -11.7937 15.3873 REMARK 3 T TENSOR REMARK 3 T11: 0.2466 T22: 0.2342 REMARK 3 T33: 0.2979 T12: -0.0014 REMARK 3 T13: -0.0763 T23: -0.0880 REMARK 3 L TENSOR REMARK 3 L11: 0.9373 L22: 0.6281 REMARK 3 L33: 1.0297 L12: 0.1679 REMARK 3 L13: 0.0477 L23: -0.5432 REMARK 3 S TENSOR REMARK 3 S11: 0.0835 S12: -0.0122 S13: -0.1790 REMARK 3 S21: 0.0903 S22: 0.0214 S23: -0.1218 REMARK 3 S31: 0.0944 S32: 0.0810 S33: -0.0981 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 399 THROUGH 573 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.1967 -13.6293 22.0451 REMARK 3 T TENSOR REMARK 3 T11: 0.2576 T22: 0.2494 REMARK 3 T33: 0.3053 T12: -0.0044 REMARK 3 T13: -0.0801 T23: -0.0436 REMARK 3 L TENSOR REMARK 3 L11: 0.7708 L22: 0.7691 REMARK 3 L33: 0.6774 L12: 0.1843 REMARK 3 L13: -0.2643 L23: -0.0915 REMARK 3 S TENSOR REMARK 3 S11: 0.0858 S12: -0.1109 S13: -0.1953 REMARK 3 S21: 0.1924 S22: 0.0073 S23: -0.0514 REMARK 3 S31: 0.0478 S32: 0.0194 S33: -0.0808 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 574 THROUGH 747 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.2914 5.6970 36.4135 REMARK 3 T TENSOR REMARK 3 T11: 0.3262 T22: 0.3538 REMARK 3 T33: 0.1885 T12: 0.0275 REMARK 3 T13: -0.0302 T23: -0.0347 REMARK 3 L TENSOR REMARK 3 L11: 1.4309 L22: 2.6687 REMARK 3 L33: 1.8932 L12: -0.4262 REMARK 3 L13: -0.4080 L23: 0.0813 REMARK 3 S TENSOR REMARK 3 S11: 0.0144 S12: -0.0694 S13: -0.0123 REMARK 3 S21: 0.3364 S22: 0.0817 S23: 0.2335 REMARK 3 S31: -0.1267 S32: -0.4100 S33: -0.0883 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 8DYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1272 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61448 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 2XIJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M BIS REMARK 280 -TRIS, PH 5.5, 16% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 98.00750 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 98.00750 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 29.68850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.03500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.68850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.03500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 98.00750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.68850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.03500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.00750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.68850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.03500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET B 11 REMARK 465 SER B 12 REMARK 465 PRO B 13 REMARK 465 HIS B 14 REMARK 465 TYR B 15 REMARK 465 LEU B 16 REMARK 465 ARG B 17 REMARK 465 GLN B 18 REMARK 465 VAL B 19 REMARK 465 LYS B 20 REMARK 465 GLU B 21 REMARK 465 SER B 22 REMARK 465 SER B 23 REMARK 465 GLY B 24 REMARK 465 SER B 25 REMARK 465 ARG B 26 REMARK 465 LEU B 27 REMARK 465 ILE B 28 REMARK 465 GLN B 29 REMARK 465 GLN B 30 REMARK 465 ARG B 31 REMARK 465 LEU B 32 REMARK 465 LEU B 33 REMARK 465 HIS B 34 REMARK 465 GLN B 35 REMARK 465 GLU B 497 REMARK 465 ASP B 498 REMARK 465 THR B 499 REMARK 465 VAL B 500 REMARK 465 GLU B 501 REMARK 465 VAL B 502 REMARK 465 LEU B 503 REMARK 465 ALA B 504 REMARK 465 ILE B 505 REMARK 465 GLN B 748 REMARK 465 SER B 749 REMARK 465 VAL B 750 REMARK 465 ALA B 751 REMARK 465 GLU B 752 REMARK 465 ASN B 753 REMARK 465 LEU B 754 REMARK 465 TYR B 755 REMARK 465 PHE B 756 REMARK 465 GLN B 757 REMARK 465 SER B 758 REMARK 465 HIS B 759 REMARK 465 HIS B 760 REMARK 465 HIS B 761 REMARK 465 HIS B 762 REMARK 465 HIS B 763 REMARK 465 HIS B 764 REMARK 465 ASP B 765 REMARK 465 TYR B 766 REMARK 465 LYS B 767 REMARK 465 ASP B 768 REMARK 465 ASP B 769 REMARK 465 ASP B 770 REMARK 465 ASP B 771 REMARK 465 LYS B 772 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 GLN B 36 CG CD OE1 NE2 REMARK 470 GLN B 37 CG CD OE1 NE2 REMARK 470 GLU B 42 CG CD OE1 OE2 REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 LYS B 54 CG CD CE NZ REMARK 470 ARG B 103 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 LYS B 128 CG CD CE NZ REMARK 470 GLN B 131 CG CD OE1 NE2 REMARK 470 ARG B 154 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 181 NZ REMARK 470 GLU B 204 CG CD OE1 OE2 REMARK 470 LYS B 210 CG CD CE NZ REMARK 470 GLU B 211 CG CD OE1 OE2 REMARK 470 LYS B 212 CG CD CE NZ REMARK 470 LYS B 251 CE NZ REMARK 470 LYS B 255 CG CD CE NZ REMARK 470 GLN B 293 CG CD OE1 NE2 REMARK 470 ARG B 304 CZ NH1 NH2 REMARK 470 LYS B 340 CE NZ REMARK 470 LYS B 343 CD CE NZ REMARK 470 GLU B 360 CG CD OE1 OE2 REMARK 470 GLU B 495 CG CD OE1 OE2 REMARK 470 LYS B 496 CG CD CE NZ REMARK 470 ILE B 515 CD1 REMARK 470 GLU B 516 CG CD OE1 OE2 REMARK 470 LYS B 519 CG CD CE NZ REMARK 470 LYS B 520 CG CD CE NZ REMARK 470 SER B 523 OG REMARK 470 SER B 524 OG REMARK 470 GLN B 527 CG CD OE1 NE2 REMARK 470 GLU B 531 CG CD OE1 OE2 REMARK 470 LYS B 571 NZ REMARK 470 LYS B 577 CG CD CE NZ REMARK 470 GLU B 593 CG CD OE1 OE2 REMARK 470 LYS B 595 CE NZ REMARK 470 LYS B 602 CG CD CE NZ REMARK 470 LYS B 606 CG CD CE NZ REMARK 470 MET B 608 CG SD CE REMARK 470 ARG B 655 CD NE CZ NH1 NH2 REMARK 470 LYS B 687 CD CE NZ REMARK 470 GLU B 711 CG CD OE1 OE2 REMARK 470 GLU B 715 CG CD OE1 OE2 REMARK 470 LYS B 730 CE NZ REMARK 470 LYS B 741 CG CD CE NZ REMARK 470 GLU B 744 CD OE1 OE2 REMARK 470 LYS B 745 CG CD CE NZ REMARK 470 LYS B 746 CG CD CE NZ REMARK 470 GLN B 747 CG CD OE1 NE2 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 MET B 99 -110.73 43.20 REMARK 500 MET B 159 -64.77 -93.95 REMARK 500 ASN B 189 -51.87 -137.03 REMARK 500 ALA B 191 40.53 -83.50 REMARK 500 VAL B 227 -29.89 -142.63 REMARK 500 ILE B 232 -60.17 -125.49 REMARK 500 ASP B 423 64.32 34.61 REMARK 500 ALA B 676 71.30 56.47 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 B12 B 801 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 627 NE2 REMARK 620 2 B12 B 801 N21 87.7 REMARK 620 3 B12 B 801 N22 88.5 94.1 REMARK 620 4 B12 B 801 N23 91.2 172.0 93.7 REMARK 620 5 B12 B 801 N24 102.8 81.7 167.8 90.9 REMARK 620 6 HOH B1045 O 176.8 95.5 91.2 85.7 77.8 REMARK 620 N 1 2 3 4 5 DBREF 8DYL B 12 750 UNP P22033 MUTA_HUMAN 12 750 SEQADV 8DYL MET B 11 UNP P22033 INITIATING METHIONINE SEQADV 8DYL THR B 499 UNP P22033 ALA 499 CONFLICT SEQADV 8DYL VAL B 671 UNP P22033 ILE 671 CONFLICT SEQADV 8DYL ALA B 751 UNP P22033 EXPRESSION TAG SEQADV 8DYL GLU B 752 UNP P22033 EXPRESSION TAG SEQADV 8DYL ASN B 753 UNP P22033 EXPRESSION TAG SEQADV 8DYL LEU B 754 UNP P22033 EXPRESSION TAG SEQADV 8DYL TYR B 755 UNP P22033 EXPRESSION TAG SEQADV 8DYL PHE B 756 UNP P22033 EXPRESSION TAG SEQADV 8DYL GLN B 757 UNP P22033 EXPRESSION TAG SEQADV 8DYL SER B 758 UNP P22033 EXPRESSION TAG SEQADV 8DYL HIS B 759 UNP P22033 EXPRESSION TAG SEQADV 8DYL HIS B 760 UNP P22033 EXPRESSION TAG SEQADV 8DYL HIS B 761 UNP P22033 EXPRESSION TAG SEQADV 8DYL HIS B 762 UNP P22033 EXPRESSION TAG SEQADV 8DYL HIS B 763 UNP P22033 EXPRESSION TAG SEQADV 8DYL HIS B 764 UNP P22033 EXPRESSION TAG SEQADV 8DYL ASP B 765 UNP P22033 EXPRESSION TAG SEQADV 8DYL TYR B 766 UNP P22033 EXPRESSION TAG SEQADV 8DYL LYS B 767 UNP P22033 EXPRESSION TAG SEQADV 8DYL ASP B 768 UNP P22033 EXPRESSION TAG SEQADV 8DYL ASP B 769 UNP P22033 EXPRESSION TAG SEQADV 8DYL ASP B 770 UNP P22033 EXPRESSION TAG SEQADV 8DYL ASP B 771 UNP P22033 EXPRESSION TAG SEQADV 8DYL LYS B 772 UNP P22033 EXPRESSION TAG SEQRES 1 B 762 MET SER PRO HIS TYR LEU ARG GLN VAL LYS GLU SER SER SEQRES 2 B 762 GLY SER ARG LEU ILE GLN GLN ARG LEU LEU HIS GLN GLN SEQRES 3 B 762 GLN PRO LEU HIS PRO GLU TRP ALA ALA LEU ALA LYS LYS SEQRES 4 B 762 GLN LEU LYS GLY LYS ASN PRO GLU ASP LEU ILE TRP HIS SEQRES 5 B 762 THR PRO GLU GLY ILE SER ILE LYS PRO LEU TYR SER LYS SEQRES 6 B 762 ARG ASP THR MET ASP LEU PRO GLU GLU LEU PRO GLY VAL SEQRES 7 B 762 LYS PRO PHE THR ARG GLY PRO TYR PRO THR MET TYR THR SEQRES 8 B 762 PHE ARG PRO TRP THR ILE ARG GLN TYR ALA GLY PHE SER SEQRES 9 B 762 THR VAL GLU GLU SER ASN LYS PHE TYR LYS ASP ASN ILE SEQRES 10 B 762 LYS ALA GLY GLN GLN GLY LEU SER VAL ALA PHE ASP LEU SEQRES 11 B 762 ALA THR HIS ARG GLY TYR ASP SER ASP ASN PRO ARG VAL SEQRES 12 B 762 ARG GLY ASP VAL GLY MET ALA GLY VAL ALA ILE ASP THR SEQRES 13 B 762 VAL GLU ASP THR LYS ILE LEU PHE ASP GLY ILE PRO LEU SEQRES 14 B 762 GLU LYS MET SER VAL SER MET THR MET ASN GLY ALA VAL SEQRES 15 B 762 ILE PRO VAL LEU ALA ASN PHE ILE VAL THR GLY GLU GLU SEQRES 16 B 762 GLN GLY VAL PRO LYS GLU LYS LEU THR GLY THR ILE GLN SEQRES 17 B 762 ASN ASP ILE LEU LYS GLU PHE MET VAL ARG ASN THR TYR SEQRES 18 B 762 ILE PHE PRO PRO GLU PRO SER MET LYS ILE ILE ALA ASP SEQRES 19 B 762 ILE PHE GLU TYR THR ALA LYS HIS MET PRO LYS PHE ASN SEQRES 20 B 762 SER ILE SER ILE SER GLY TYR HIS MET GLN GLU ALA GLY SEQRES 21 B 762 ALA ASP ALA ILE LEU GLU LEU ALA TYR THR LEU ALA ASP SEQRES 22 B 762 GLY LEU GLU TYR SER ARG THR GLY LEU GLN ALA GLY LEU SEQRES 23 B 762 THR ILE ASP GLU PHE ALA PRO ARG LEU SER PHE PHE TRP SEQRES 24 B 762 GLY ILE GLY MET ASN PHE TYR MET GLU ILE ALA LYS MET SEQRES 25 B 762 ARG ALA GLY ARG ARG LEU TRP ALA HIS LEU ILE GLU LYS SEQRES 26 B 762 MET PHE GLN PRO LYS ASN SER LYS SER LEU LEU LEU ARG SEQRES 27 B 762 ALA HIS CYS GLN THR SER GLY TRP SER LEU THR GLU GLN SEQRES 28 B 762 ASP PRO TYR ASN ASN ILE VAL ARG THR ALA ILE GLU ALA SEQRES 29 B 762 MET ALA ALA VAL PHE GLY GLY THR GLN SER LEU HIS THR SEQRES 30 B 762 ASN SER PHE ASP GLU ALA LEU GLY LEU PRO THR VAL LYS SEQRES 31 B 762 SER ALA ARG ILE ALA ARG ASN THR GLN ILE ILE ILE GLN SEQRES 32 B 762 GLU GLU SER GLY ILE PRO LYS VAL ALA ASP PRO TRP GLY SEQRES 33 B 762 GLY SER TYR MET MET GLU CYS LEU THR ASN ASP VAL TYR SEQRES 34 B 762 ASP ALA ALA LEU LYS LEU ILE ASN GLU ILE GLU GLU MET SEQRES 35 B 762 GLY GLY MET ALA LYS ALA VAL ALA GLU GLY ILE PRO LYS SEQRES 36 B 762 LEU ARG ILE GLU GLU CYS ALA ALA ARG ARG GLN ALA ARG SEQRES 37 B 762 ILE ASP SER GLY SER GLU VAL ILE VAL GLY VAL ASN LYS SEQRES 38 B 762 TYR GLN LEU GLU LYS GLU ASP THR VAL GLU VAL LEU ALA SEQRES 39 B 762 ILE ASP ASN THR SER VAL ARG ASN ARG GLN ILE GLU LYS SEQRES 40 B 762 LEU LYS LYS ILE LYS SER SER ARG ASP GLN ALA LEU ALA SEQRES 41 B 762 GLU ARG CYS LEU ALA ALA LEU THR GLU CYS ALA ALA SER SEQRES 42 B 762 GLY ASP GLY ASN ILE LEU ALA LEU ALA VAL ASP ALA SER SEQRES 43 B 762 ARG ALA ARG CYS THR VAL GLY GLU ILE THR ASP ALA LEU SEQRES 44 B 762 LYS LYS VAL PHE GLY GLU HIS LYS ALA ASN ASP ARG MET SEQRES 45 B 762 VAL SER GLY ALA TYR ARG GLN GLU PHE GLY GLU SER LYS SEQRES 46 B 762 GLU ILE THR SER ALA ILE LYS ARG VAL HIS LYS PHE MET SEQRES 47 B 762 GLU ARG GLU GLY ARG ARG PRO ARG LEU LEU VAL ALA LYS SEQRES 48 B 762 MET GLY GLN ASP GLY HIS ASP ARG GLY ALA LYS VAL ILE SEQRES 49 B 762 ALA THR GLY PHE ALA ASP LEU GLY PHE ASP VAL ASP ILE SEQRES 50 B 762 GLY PRO LEU PHE GLN THR PRO ARG GLU VAL ALA GLN GLN SEQRES 51 B 762 ALA VAL ASP ALA ASP VAL HIS ALA VAL GLY VAL SER THR SEQRES 52 B 762 LEU ALA ALA GLY HIS LYS THR LEU VAL PRO GLU LEU ILE SEQRES 53 B 762 LYS GLU LEU ASN SER LEU GLY ARG PRO ASP ILE LEU VAL SEQRES 54 B 762 MET CYS GLY GLY VAL ILE PRO PRO GLN ASP TYR GLU PHE SEQRES 55 B 762 LEU PHE GLU VAL GLY VAL SER ASN VAL PHE GLY PRO GLY SEQRES 56 B 762 THR ARG ILE PRO LYS ALA ALA VAL GLN VAL LEU ASP ASP SEQRES 57 B 762 ILE GLU LYS CYS LEU GLU LYS LYS GLN GLN SER VAL ALA SEQRES 58 B 762 GLU ASN LEU TYR PHE GLN SER HIS HIS HIS HIS HIS HIS SEQRES 59 B 762 ASP TYR LYS ASP ASP ASP ASP LYS HET B12 B 801 91 HET GOL B 802 6 HET GOL B 803 6 HET GOL B 804 6 HET GOL B 805 6 HET GOL B 806 6 HET GOL B 807 6 HETNAM B12 COBALAMIN HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 B12 C62 H89 CO N13 O14 P 2+ FORMUL 3 GOL 6(C3 H8 O3) FORMUL 9 HOH *246(H2 O) HELIX 1 AA1 HIS B 40 LEU B 51 1 12 HELIX 2 AA2 ASN B 55 ILE B 60 5 6 HELIX 3 AA3 SER B 74 THR B 78 5 5 HELIX 4 AA4 THR B 115 ALA B 129 1 15 HELIX 5 AA5 ASP B 139 ARG B 144 1 6 HELIX 6 AA6 ASN B 150 ARG B 154 5 5 HELIX 7 AA7 THR B 166 PHE B 174 1 9 HELIX 8 AA8 ALA B 191 GLN B 206 1 16 HELIX 9 AA9 PRO B 209 LEU B 213 5 5 HELIX 10 AB1 ASP B 220 VAL B 227 1 8 HELIX 11 AB2 PRO B 234 MET B 253 1 20 HELIX 12 AB3 GLY B 263 ALA B 269 1 7 HELIX 13 AB4 ASP B 272 ALA B 294 1 23 HELIX 14 AB5 THR B 297 ALA B 302 1 6 HELIX 15 AB6 ASN B 314 GLN B 338 1 25 HELIX 16 AB7 ASN B 341 LEU B 346 5 6 HELIX 17 AB8 TYR B 364 GLY B 380 1 17 HELIX 18 AB9 THR B 398 GLU B 415 1 18 HELIX 19 AC1 GLY B 417 VAL B 421 5 5 HELIX 20 AC2 SER B 428 MET B 452 1 25 HELIX 21 AC3 GLY B 454 GLY B 462 1 9 HELIX 22 AC4 GLY B 462 SER B 481 1 20 HELIX 23 AC5 ASN B 507 ARG B 525 1 19 HELIX 24 AC6 ASP B 526 GLY B 544 1 19 HELIX 25 AC7 ASN B 547 ALA B 558 1 12 HELIX 26 AC8 THR B 561 GLY B 574 1 14 HELIX 27 AC9 GLY B 585 GLY B 592 1 8 HELIX 28 AD1 SER B 594 GLY B 612 1 19 HELIX 29 AD2 ASP B 628 LEU B 641 1 14 HELIX 30 AD3 THR B 653 ALA B 664 1 12 HELIX 31 AD4 GLY B 677 LEU B 692 1 16 HELIX 32 AD5 PRO B 706 GLN B 708 5 3 HELIX 33 AD6 ASP B 709 GLY B 717 1 9 HELIX 34 AD7 ARG B 727 LYS B 746 1 20 SHEET 1 AA1 2 TRP B 61 HIS B 62 0 SHEET 2 AA1 2 SER B 68 ILE B 69 -1 O ILE B 69 N TRP B 61 SHEET 1 AA2 5 THR B 106 ILE B 107 0 SHEET 2 AA2 5 SER B 384 HIS B 386 1 O LEU B 385 N THR B 106 SHEET 3 AA2 5 ALA B 349 THR B 353 1 N THR B 353 O HIS B 386 SHEET 4 AA2 5 LEU B 305 ILE B 311 1 N PHE B 307 O HIS B 350 SHEET 5 AA2 5 ILE B 259 SER B 262 1 N ILE B 261 O SER B 306 SHEET 1 AA3 3 GLY B 133 VAL B 136 0 SHEET 2 AA3 3 SER B 183 MET B 186 1 O SER B 183 N LEU B 134 SHEET 3 AA3 3 THR B 214 ILE B 217 1 O THR B 216 N MET B 186 SHEET 1 AA4 5 ASP B 644 ILE B 647 0 SHEET 2 AA4 5 ARG B 616 ALA B 620 1 N VAL B 619 O ASP B 646 SHEET 3 AA4 5 ALA B 668 THR B 673 1 O GLY B 670 N LEU B 618 SHEET 4 AA4 5 LEU B 698 GLY B 703 1 O MET B 700 N VAL B 671 SHEET 5 AA4 5 ASN B 720 PHE B 722 1 O PHE B 722 N CYS B 701 LINK NE2 HIS B 627 CO B12 B 801 1555 1555 2.30 LINK CO B12 B 801 O HOH B1045 1555 1555 2.49 CISPEP 1 LYS B 89 PRO B 90 0 6.60 CRYST1 59.377 136.070 196.015 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 0.016842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005102 0.00000