HEADER METAL BINDING PROTEIN 22-SEP-23 8QMK TITLE ENZYMATICALLY-PRODUCED COMPLEX-B BOUND TMHYDE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: [FEFE] HYDROGENASE MATURASE SUBUNIT HYDE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.8.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA MSB8; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 GENE: TM_1269, THEMA_07990, TMARI_1274; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS [FEFE]-HYDROGENASE, H-CLUSTER, COMPLEX-B, MATURASE, HYDE, IRON-SULFUR KEYWDS 2 CLUSTER, RADICAL SAM PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.OMEIRI,L.MARTIN,A.USCLAT,M.V.CHERRIER,Y.NICOLET REVDAT 4 27-DEC-23 8QMK 1 JRNL REVDAT 3 20-DEC-23 8QMK 1 JRNL REVDAT 2 06-DEC-23 8QMK 1 JRNL REVDAT 1 22-NOV-23 8QMK 0 JRNL AUTH J.OMEIRI,L.MARTIN,A.USCLAT,M.V.CHERRIER,Y.NICOLET JRNL TITL MATURATION OF THE [FEFE]-HYDROGENASE: DIRECT TRANSFER OF THE JRNL TITL 2 ( KAPPA 3 -CYSTEINATE)FE II (CN)(CO) 2 COMPLEX B FROM HYDG JRNL TITL 3 TO HYDE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 14819 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 37962296 JRNL DOI 10.1002/ANIE.202314819 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 179824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 9005 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 34.9600 - 4.0400 1.00 5706 307 0.1256 0.1384 REMARK 3 2 4.0400 - 3.2100 1.00 5669 305 0.1092 0.1265 REMARK 3 3 3.2100 - 2.8000 1.00 5707 299 0.1194 0.1324 REMARK 3 4 2.8000 - 2.5400 1.00 5704 296 0.1291 0.1723 REMARK 3 5 2.5400 - 2.3600 1.00 5704 299 0.1238 0.1649 REMARK 3 6 2.3600 - 2.2200 1.00 5699 300 0.1218 0.1419 REMARK 3 7 2.2200 - 2.1100 1.00 5693 299 0.1211 0.1652 REMARK 3 8 2.1100 - 2.0200 1.00 5684 295 0.1293 0.1660 REMARK 3 9 2.0200 - 1.9400 1.00 5702 304 0.1214 0.1546 REMARK 3 10 1.9400 - 1.8700 1.00 5694 298 0.1312 0.1556 REMARK 3 11 1.8700 - 1.8200 1.00 5692 296 0.1227 0.1450 REMARK 3 12 1.8200 - 1.7600 1.00 5683 304 0.1297 0.1546 REMARK 3 13 1.7600 - 1.7200 1.00 5730 299 0.1425 0.1823 REMARK 3 14 1.7200 - 1.6800 1.00 5709 304 0.1409 0.1787 REMARK 3 15 1.6800 - 1.6400 1.00 5715 296 0.1442 0.1549 REMARK 3 16 1.6400 - 1.6000 1.00 5694 300 0.1471 0.1819 REMARK 3 17 1.6000 - 1.5700 1.00 5708 298 0.1515 0.1749 REMARK 3 18 1.5700 - 1.5400 1.00 5650 300 0.1585 0.2005 REMARK 3 19 1.5400 - 1.5100 1.00 5746 306 0.1797 0.1993 REMARK 3 20 1.5100 - 1.4900 1.00 5666 299 0.1767 0.1711 REMARK 3 21 1.4900 - 1.4600 1.00 5707 301 0.2079 0.2156 REMARK 3 22 1.4600 - 1.4400 1.00 5617 296 0.2329 0.2803 REMARK 3 23 1.4400 - 1.4200 1.00 5751 299 0.2322 0.2740 REMARK 3 24 1.4200 - 1.4000 1.00 5719 306 0.2447 0.2569 REMARK 3 25 1.4000 - 1.3800 1.00 5681 300 0.2711 0.2944 REMARK 3 26 1.3800 - 1.3600 0.98 5537 296 0.3100 0.3430 REMARK 3 27 1.3600 - 1.3500 1.00 5724 298 0.2804 0.2991 REMARK 3 28 1.3500 - 1.3300 1.00 5748 307 0.2853 0.3014 REMARK 3 29 1.3300 - 1.3100 1.00 5653 298 0.2941 0.3124 REMARK 3 30 1.3100 - 1.3000 0.99 5727 300 0.3214 0.3341 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) : 0.142 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.003 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.87 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 : 0.022 3275 REMARK 3 ANGLE : 1.788 4495 REMARK 3 CHIRALITY : 0.162 495 REMARK 3 PLANARITY : 0.019 576 REMARK 3 DIHEDRAL : 21.830 1339 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -8 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.6247 14.4035 -21.2122 REMARK 3 T TENSOR REMARK 3 T11: 0.1863 T22: 0.3297 REMARK 3 T33: 0.3031 T12: -0.0375 REMARK 3 T13: -0.0745 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 7.8879 L22: 1.3748 REMARK 3 L33: 3.6813 L12: -0.3830 REMARK 3 L13: -4.9429 L23: -0.1595 REMARK 3 S TENSOR REMARK 3 S11: -0.0391 S12: -0.3319 S13: -0.2718 REMARK 3 S21: -0.1060 S22: 0.0156 S23: -0.2120 REMARK 3 S31: 0.0746 S32: 0.5210 S33: 0.0773 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0673 15.4222 -15.7107 REMARK 3 T TENSOR REMARK 3 T11: 0.1069 T22: 0.0464 REMARK 3 T33: 0.1079 T12: -0.0130 REMARK 3 T13: -0.0073 T23: 0.0160 REMARK 3 L TENSOR REMARK 3 L11: 1.9990 L22: 0.2612 REMARK 3 L33: 1.2163 L12: -0.0922 REMARK 3 L13: 0.3376 L23: 0.0299 REMARK 3 S TENSOR REMARK 3 S11: -0.0147 S12: -0.0910 S13: 0.0223 REMARK 3 S21: 0.0235 S22: -0.0027 S23: -0.0763 REMARK 3 S31: -0.0560 S32: 0.1756 S33: 0.0059 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.7180 17.0845 -17.8893 REMARK 3 T TENSOR REMARK 3 T11: 0.0983 T22: 0.1291 REMARK 3 T33: 0.1077 T12: 0.0144 REMARK 3 T13: 0.0033 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.0453 L22: 0.8100 REMARK 3 L33: 2.8602 L12: -0.1725 REMARK 3 L13: -0.1920 L23: 0.5560 REMARK 3 S TENSOR REMARK 3 S11: -0.0284 S12: -0.0106 S13: -0.0051 REMARK 3 S21: 0.0354 S22: -0.0139 S23: 0.0990 REMARK 3 S31: -0.0597 S32: -0.2631 S33: 0.0476 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.3396 26.3929 -25.3480 REMARK 3 T TENSOR REMARK 3 T11: 0.1526 T22: 0.0748 REMARK 3 T33: 0.1104 T12: 0.0063 REMARK 3 T13: -0.0010 T23: 0.0174 REMARK 3 L TENSOR REMARK 3 L11: 1.0773 L22: 0.3558 REMARK 3 L33: 1.6727 L12: -0.1445 REMARK 3 L13: -0.3920 L23: 0.0680 REMARK 3 S TENSOR REMARK 3 S11: 0.0206 S12: 0.0575 S13: 0.1350 REMARK 3 S21: -0.0309 S22: -0.0177 S23: -0.0050 REMARK 3 S31: -0.2565 S32: 0.0101 S33: -0.0154 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 299 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0157 13.7814 -19.3159 REMARK 3 T TENSOR REMARK 3 T11: 0.1112 T22: 0.0846 REMARK 3 T33: 0.1017 T12: -0.0041 REMARK 3 T13: -0.0029 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.8681 L22: 0.2884 REMARK 3 L33: 0.9568 L12: -0.1616 REMARK 3 L13: -0.0170 L23: -0.0916 REMARK 3 S TENSOR REMARK 3 S11: 0.0089 S12: 0.0183 S13: -0.0094 REMARK 3 S21: -0.0249 S22: -0.0216 S23: -0.0243 REMARK 3 S31: -0.0115 S32: 0.0499 S33: 0.0112 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 317 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1449 2.7140 -17.0753 REMARK 3 T TENSOR REMARK 3 T11: 0.1268 T22: 0.1230 REMARK 3 T33: 0.1656 T12: -0.0066 REMARK 3 T13: -0.0191 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 3.3805 L22: 3.5351 REMARK 3 L33: 1.3812 L12: -2.1751 REMARK 3 L13: -1.0569 L23: 1.8704 REMARK 3 S TENSOR REMARK 3 S11: -0.1531 S12: -0.2492 S13: -0.3457 REMARK 3 S21: 0.1203 S22: 0.1879 S23: 0.1529 REMARK 3 S31: 0.2504 S32: 0.0669 S33: -0.0183 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 318 THROUGH 401 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.8384 15.3922 -3.2182 REMARK 3 T TENSOR REMARK 3 T11: 0.1178 T22: 0.1742 REMARK 3 T33: 0.0908 T12: 0.0241 REMARK 3 T13: 0.0061 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.9833 L22: 2.1671 REMARK 3 L33: 2.4949 L12: 0.4318 REMARK 3 L13: 0.3395 L23: 0.1978 REMARK 3 S TENSOR REMARK 3 S11: -0.0172 S12: -0.3795 S13: -0.1013 REMARK 3 S21: 0.1525 S22: 0.0462 S23: -0.1275 REMARK 3 S31: -0.0167 S32: 0.0944 S33: -0.0280 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 8QMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292133507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-22 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87313 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 179824 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS PH=8, LISO4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.91500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.91500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.78000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 THR A 347 REMARK 465 VAL A 348 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 -1 CD CE NZ REMARK 470 LYS A 315 CE NZ REMARK 470 LYS A 325 CD CE NZ REMARK 470 ARG A 336 CD NE CZ NH1 NH2 REMARK 470 GLU A 346 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 FE FE2 A 501 C CYN A 504 1.83 REMARK 500 OD1 ASP A 49 O HOH A 601 1.96 REMARK 500 O HOH A 662 O HOH A 892 1.97 REMARK 500 O HOH A 800 O HOH A 1023 2.15 REMARK 500 O HOH A 770 O HOH A 1028 2.15 REMARK 500 ND1 HIS A -6 O HOH A 602 2.18 REMARK 500 OE1 GLU A 150 O HOH A 603 2.18 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 GLU A 346 O HOH A 1058 4555 2.12 REMARK 500 O HOH A 971 O HOH A 1077 4554 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 45 CE LYS A 45 NZ -0.151 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 ASP A 49 CB - CG - OD1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ASP A 49 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 117 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 337 CB - CG - OD1 ANGL. DEV. = 6.6 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 13 33.61 71.62 REMARK 500 PHE A 15 57.01 -94.70 REMARK 500 ASN A 27 75.91 -112.54 REMARK 500 ASN A 78 36.85 -91.37 REMARK 500 GLU A 161 -61.53 74.19 REMARK 500 THR A 175 -153.74 -152.03 REMARK 500 ALA A 196 -153.29 -117.94 REMARK 500 ASN A 288 14.20 -142.92 REMARK 500 ASP A 337 -157.08 -126.77 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 A1067 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A1068 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A1069 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A1070 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A1071 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A1072 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A1073 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A1074 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A1075 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A1076 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A1077 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH A1078 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A1079 DISTANCE = 8.55 ANGSTROMS REMARK 525 HOH A1080 DISTANCE = 9.34 ANGSTROMS REMARK 525 HOH A1081 DISTANCE = 10.00 ANGSTROMS REMARK 525 HOH A1082 DISTANCE = 10.93 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CPS A 505 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 SF4 A 506 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 SF4 A 506 S1 104.9 REMARK 620 3 SF4 A 506 S3 116.2 106.2 REMARK 620 4 SF4 A 506 S4 118.9 104.3 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 506 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 SF4 A 506 S1 116.8 REMARK 620 3 SF4 A 506 S2 116.5 103.1 REMARK 620 4 SF4 A 506 S4 108.1 104.8 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 506 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 70 SG REMARK 620 2 SF4 A 506 S2 109.6 REMARK 620 3 SF4 A 506 S3 120.8 105.0 REMARK 620 4 SF4 A 506 S4 109.4 106.4 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 511 N REMARK 620 2 CYS A 511 SG 83.2 REMARK 620 3 CYS A 511 O 74.0 83.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 506 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAH A 507 N REMARK 620 2 SF4 A 506 S1 95.9 REMARK 620 3 SF4 A 506 S2 161.7 98.2 REMARK 620 4 SF4 A 506 S3 89.4 100.5 99.4 REMARK 620 5 SAH A 507 OXT 72.7 95.7 94.2 157.0 REMARK 620 N 1 2 3 4 DBREF 8QMK A 2 348 UNP Q9X0Z6 HYDE_THEMA 2 348 SEQADV 8QMK MET A -9 UNP Q9X0Z6 INITIATING METHIONINE SEQADV 8QMK TRP A -8 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK SER A -7 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK HIS A -6 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK PRO A -5 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK GLN A -4 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK PHE A -3 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK GLU A -2 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK LYS A -1 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK ALA A 0 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK SER A 1 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QMK ILE A 291 UNP Q9X0Z6 MET 291 ENGINEERED MUTATION SEQADV 8QMK SER A 311 UNP Q9X0Z6 CYS 311 ENGINEERED MUTATION SEQADV 8QMK SER A 319 UNP Q9X0Z6 CYS 319 ENGINEERED MUTATION SEQADV 8QMK SER A 322 UNP Q9X0Z6 CYS 322 ENGINEERED MUTATION SEQRES 1 A 358 MET TRP SER HIS PRO GLN PHE GLU LYS ALA SER THR GLY SEQRES 2 A 358 ARG GLU ILE LEU GLU LYS LEU GLU ARG ARG GLU PHE THR SEQRES 3 A 358 ARG GLU VAL LEU LYS GLU ALA LEU SER ILE ASN ASP ARG SEQRES 4 A 358 GLY PHE ASN GLU ALA LEU PHE LYS LEU ALA ASP GLU ILE SEQRES 5 A 358 ARG ARG LYS TYR VAL GLY ASP GLU VAL HIS ILE ARG ALA SEQRES 6 A 358 ILE ILE GLU PHE SER ASN VAL CYS ARG LYS ASN CYS LEU SEQRES 7 A 358 TYR CYS GLY LEU ARG ARG ASP ASN LYS ASN LEU LYS ARG SEQRES 8 A 358 TYR ARG MET THR PRO GLU GLU ILE VAL GLU ARG ALA ARG SEQRES 9 A 358 LEU ALA VAL GLN PHE GLY ALA LYS THR ILE VAL LEU GLN SEQRES 10 A 358 SER GLY GLU ASP PRO TYR TYR MET PRO ASP VAL ILE SER SEQRES 11 A 358 ASP ILE VAL LYS GLU ILE LYS LYS MET GLY VAL ALA VAL SEQRES 12 A 358 THR LEU SER LEU GLY GLU TRP PRO ARG GLU TYR TYR GLU SEQRES 13 A 358 LYS TRP LYS GLU ALA GLY ALA ASP ARG TYR LEU LEU ARG SEQRES 14 A 358 HIS GLU THR ALA ASN PRO VAL LEU HIS ARG LYS LEU ARG SEQRES 15 A 358 PRO ASP THR SER PHE GLU ASN ARG LEU ASN CYS LEU LEU SEQRES 16 A 358 THR LEU LYS GLU LEU GLY TYR GLU THR GLY ALA GLY SER SEQRES 17 A 358 MET VAL GLY LEU PRO GLY GLN THR ILE ASP ASP LEU VAL SEQRES 18 A 358 ASP ASP LEU LEU PHE LEU LYS GLU HIS ASP PHE ASP MET SEQRES 19 A 358 VAL GLY ILE GLY PRO PHE ILE PRO HIS PRO ASP THR PRO SEQRES 20 A 358 LEU ALA ASN GLU LYS LYS GLY ASP PHE THR LEU THR LEU SEQRES 21 A 358 LYS MET VAL ALA LEU THR ARG ILE LEU LEU PRO ASP SER SEQRES 22 A 358 ASN ILE PRO ALA THR THR ALA MET GLY THR ILE VAL PRO SEQRES 23 A 358 GLY GLY ARG GLU ILE THR LEU ARG CYS GLY ALA ASN VAL SEQRES 24 A 358 ILE ILE PRO ASN TRP THR PRO SER PRO TYR ARG GLN LEU SEQRES 25 A 358 TYR GLN LEU TYR PRO GLY LYS ILE SER VAL PHE GLU LYS SEQRES 26 A 358 ASP THR ALA SER ILE PRO SER VAL MET LYS MET ILE GLU SEQRES 27 A 358 LEU LEU GLY ARG LYS PRO GLY ARG ASP TRP GLY GLY ARG SEQRES 28 A 358 LYS ARG VAL PHE GLU THR VAL HET FE2 A 501 1 HET CMO A 502 2 HET CMO A 503 2 HET CYN A 504 2 HET CPS A 505 23 HET SF4 A 506 8 HET SAH A 507 26 HET CL A 508 1 HET CL A 509 1 HET SO4 A 510 10 HET CYS A 511 11 HETNAM FE2 FE (II) ION HETNAM CMO CARBON MONOXIDE HETNAM CYN CYANIDE ION HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM CYS CYSTEINE HETSYN CPS CHAPS FORMUL 2 FE2 FE 2+ FORMUL 3 CMO 2(C O) FORMUL 5 CYN C N 1- FORMUL 6 CPS C32 H58 N2 O7 S FORMUL 7 SF4 FE4 S4 FORMUL 8 SAH C14 H20 N6 O5 S FORMUL 9 CL 2(CL 1-) FORMUL 11 SO4 O4 S 2- FORMUL 12 CYS C3 H7 N O2 S FORMUL 13 HOH *482(H2 O) HELIX 1 AA1 GLU A -2 ARG A 12 1 15 HELIX 2 AA2 THR A 16 ILE A 26 1 11 HELIX 3 AA3 ASP A 28 VAL A 47 1 20 HELIX 4 AA4 THR A 85 PHE A 99 1 15 HELIX 5 AA5 ASP A 111 MET A 115 5 5 HELIX 6 AA6 PRO A 116 LYS A 128 1 13 HELIX 7 AA7 PRO A 141 GLY A 152 1 12 HELIX 8 AA8 ASN A 164 ARG A 172 1 9 HELIX 9 AA9 SER A 176 LEU A 190 1 15 HELIX 10 AB1 THR A 206 ASP A 221 1 16 HELIX 11 AB2 ASP A 245 LEU A 260 1 16 HELIX 12 AB3 THR A 268 VAL A 275 1 8 HELIX 13 AB4 GLY A 277 ARG A 284 1 8 HELIX 14 AB5 TYR A 299 TYR A 303 5 5 HELIX 15 AB6 ALA A 318 LEU A 330 1 13 SHEET 1 AA1 7 MET A 224 VAL A 225 0 SHEET 2 AA1 7 GLU A 193 ALA A 196 1 N ALA A 196 O MET A 224 SHEET 3 AA1 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLY A 195 SHEET 4 AA1 7 ALA A 132 SER A 136 1 N LEU A 135 O ARG A 155 SHEET 5 AA1 7 THR A 103 SER A 108 1 N LEU A 106 O THR A 134 SHEET 6 AA1 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105 SHEET 7 AA1 7 VAL A 289 ILE A 290 1 O ILE A 290 N HIS A 52 SHEET 1 AA2 7 MET A 224 VAL A 225 0 SHEET 2 AA2 7 GLU A 193 ALA A 196 1 N ALA A 196 O MET A 224 SHEET 3 AA2 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLY A 195 SHEET 4 AA2 7 ALA A 132 SER A 136 1 N LEU A 135 O ARG A 155 SHEET 5 AA2 7 THR A 103 SER A 108 1 N LEU A 106 O THR A 134 SHEET 6 AA2 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105 SHEET 7 AA2 7 LYS A 333 PRO A 334 1 O LYS A 333 N VAL A 51 SHEET 1 AA3 2 MET A 199 VAL A 200 0 SHEET 2 AA3 2 GLY A 228 PRO A 229 1 O GLY A 228 N VAL A 200 LINK SG CYS A 63 FE2 SF4 A 506 1555 1555 2.25 LINK SG CYS A 67 FE3 SF4 A 506 1555 1555 2.34 LINK SG CYS A 70 FE1 SF4 A 506 1555 1555 2.31 LINK FE AFE2 A 501 N CYS A 511 1555 1555 2.00 LINK FE AFE2 A 501 SG CYS A 511 1555 1555 2.36 LINK FE AFE2 A 501 O CYS A 511 1555 1555 2.11 LINK FE4 SF4 A 506 N SAH A 507 1555 1555 2.31 LINK FE4 SF4 A 506 OXT SAH A 507 1555 1555 2.18 CISPEP 1 MET A 115 PRO A 116 0 -2.97 CISPEP 2 SER A 297 PRO A 298 0 5.76 CRYST1 63.830 83.560 70.840 90.00 90.00 90.00 P 21 21 2 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 0.015667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014116 0.00000