HEADER METAL BINDING PROTEIN 22-SEP-23 8QML TITLE (2R,4R)-METDA BOUND HYDE STRUCTURE (CONTROL EXPERIMENT) 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, RADICAL SAM ENZYME, HYDE, MATURASE, COMPLEX-B, H- KEYWDS 2 CLUSTER, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.OMEIRI,L.MARTIN,A.USCLAT,M.V.CHERRIER,Y.NICOLET REVDAT 4 27-DEC-23 8QML 1 JRNL REVDAT 3 20-DEC-23 8QML 1 JRNL REVDAT 2 06-DEC-23 8QML 1 JRNL REVDAT 1 22-NOV-23 8QML 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 129324 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 6373 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 23.1400 - 4.3400 1.00 4129 192 0.1309 0.1669 REMARK 3 2 4.3400 - 3.4500 1.00 4117 203 0.1110 0.1388 REMARK 3 3 3.4500 - 3.0100 1.00 4107 216 0.1312 0.1717 REMARK 3 4 3.0100 - 2.7400 1.00 4096 220 0.1467 0.1767 REMARK 3 5 2.7400 - 2.5400 1.00 4094 224 0.1519 0.1943 REMARK 3 6 2.5400 - 2.3900 1.00 4111 218 0.1509 0.2142 REMARK 3 7 2.3900 - 2.2700 1.00 4116 215 0.1389 0.2020 REMARK 3 8 2.2700 - 2.1800 1.00 4118 210 0.1467 0.1644 REMARK 3 9 2.1700 - 2.0900 1.00 4112 211 0.1395 0.1954 REMARK 3 10 2.0900 - 2.0200 1.00 4060 219 0.1431 0.1732 REMARK 3 11 2.0200 - 1.9600 1.00 4129 221 0.1485 0.2048 REMARK 3 12 1.9600 - 1.9000 1.00 4145 206 0.1557 0.1809 REMARK 3 13 1.9000 - 1.8500 1.00 4061 219 0.1593 0.2216 REMARK 3 14 1.8500 - 1.8100 1.00 4121 208 0.1510 0.2398 REMARK 3 15 1.8100 - 1.7600 1.00 4101 219 0.1650 0.1923 REMARK 3 16 1.7600 - 1.7300 1.00 4141 220 0.1677 0.1976 REMARK 3 17 1.7300 - 1.6900 1.00 4046 213 0.1907 0.1981 REMARK 3 18 1.6900 - 1.6600 0.97 4043 214 0.2877 0.3346 REMARK 3 19 1.6600 - 1.6300 0.99 4067 202 0.2338 0.2730 REMARK 3 20 1.6300 - 1.6000 1.00 4128 210 0.2541 0.2707 REMARK 3 21 1.6000 - 1.5800 1.00 4073 223 0.2302 0.2655 REMARK 3 22 1.5800 - 1.5500 1.00 4118 198 0.2229 0.2801 REMARK 3 23 1.5500 - 1.5300 1.00 4075 217 0.2383 0.2133 REMARK 3 24 1.5300 - 1.5100 1.00 4138 210 0.2562 0.2831 REMARK 3 25 1.5100 - 1.4900 1.00 4094 219 0.2851 0.3036 REMARK 3 26 1.4900 - 1.4700 1.00 4077 219 0.2909 0.3000 REMARK 3 27 1.4700 - 1.4500 0.99 4154 200 0.3372 0.3649 REMARK 3 28 1.4500 - 1.4300 0.99 4066 193 0.3563 0.3754 REMARK 3 29 1.4300 - 1.4200 0.99 4128 220 0.3712 0.4591 REMARK 3 30 1.4200 - 1.4000 0.98 3986 214 0.3555 0.3271 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.277 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.51 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 : 0.014 3543 REMARK 3 ANGLE : 1.788 4955 REMARK 3 CHIRALITY : 0.121 589 REMARK 3 PLANARITY : 0.018 607 REMARK 3 DIHEDRAL : 19.617 1537 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 2 THROUGH 28 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.7108 -13.5440 -2.7871 REMARK 3 T TENSOR REMARK 3 T11: 0.5149 T22: 0.2539 REMARK 3 T33: 0.3948 T12: 0.1305 REMARK 3 T13: 0.1033 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 3.9162 L22: 3.8581 REMARK 3 L33: 4.6848 L12: 1.4643 REMARK 3 L13: -0.3349 L23: 0.8587 REMARK 3 S TENSOR REMARK 3 S11: -0.3615 S12: -0.1662 S13: -0.7367 REMARK 3 S21: -0.4946 S22: 0.1357 S23: -0.3278 REMARK 3 S31: 0.9398 S32: 0.4005 S33: 0.2216 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 29 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.1950 -0.9110 -7.6371 REMARK 3 T TENSOR REMARK 3 T11: 0.2318 T22: 0.1487 REMARK 3 T33: 0.1982 T12: 0.0115 REMARK 3 T13: 0.0117 T23: -0.0218 REMARK 3 L TENSOR REMARK 3 L11: 6.3422 L22: 2.1537 REMARK 3 L33: 3.9582 L12: -1.7313 REMARK 3 L13: -0.9216 L23: 0.2521 REMARK 3 S TENSOR REMARK 3 S11: 0.0484 S12: 0.2296 S13: -0.0529 REMARK 3 S21: -0.2277 S22: -0.0564 S23: -0.1058 REMARK 3 S31: 0.1513 S32: 0.0080 S33: 0.1023 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.8327 8.3091 16.9479 REMARK 3 T TENSOR REMARK 3 T11: 0.1373 T22: 0.1823 REMARK 3 T33: 0.1357 T12: -0.0215 REMARK 3 T13: -0.0027 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.1483 L22: 1.0717 REMARK 3 L33: 1.9741 L12: -0.0217 REMARK 3 L13: -0.5334 L23: -0.2724 REMARK 3 S TENSOR REMARK 3 S11: 0.0133 S12: -0.2418 S13: -0.0379 REMARK 3 S21: 0.1201 S22: -0.0035 S23: 0.0752 REMARK 3 S31: -0.0104 S32: 0.1097 S33: 0.0017 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 165 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.7863 -9.4702 19.1587 REMARK 3 T TENSOR REMARK 3 T11: 0.3451 T22: 0.2629 REMARK 3 T33: 0.2970 T12: 0.0463 REMARK 3 T13: 0.0597 T23: 0.1158 REMARK 3 L TENSOR REMARK 3 L11: 2.3333 L22: 1.3357 REMARK 3 L33: 3.0330 L12: -1.2071 REMARK 3 L13: 0.4915 L23: -0.5040 REMARK 3 S TENSOR REMARK 3 S11: -0.1755 S12: -0.4756 S13: -0.5140 REMARK 3 S21: 0.1149 S22: 0.0180 S23: 0.1160 REMARK 3 S31: 0.6667 S32: 0.2735 S33: 0.0476 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 190 THROUGH 299 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.7284 1.6069 9.2464 REMARK 3 T TENSOR REMARK 3 T11: 0.1625 T22: 0.2122 REMARK 3 T33: 0.1624 T12: 0.0124 REMARK 3 T13: -0.0209 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.1952 L22: 0.7439 REMARK 3 L33: 1.5053 L12: -0.0244 REMARK 3 L13: -0.6715 L23: -0.1392 REMARK 3 S TENSOR REMARK 3 S11: -0.0345 S12: -0.2720 S13: -0.1196 REMARK 3 S21: 0.0454 S22: -0.0157 S23: -0.0810 REMARK 3 S31: 0.1947 S32: 0.3093 S33: 0.0391 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 300 THROUGH 317 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.3721 17.7526 16.5186 REMARK 3 T TENSOR REMARK 3 T11: 0.3415 T22: 0.5019 REMARK 3 T33: 0.3517 T12: -0.1084 REMARK 3 T13: 0.0446 T23: -0.0902 REMARK 3 L TENSOR REMARK 3 L11: 2.6569 L22: 1.4574 REMARK 3 L33: 0.2830 L12: -1.8548 REMARK 3 L13: 0.4070 L23: -0.4745 REMARK 3 S TENSOR REMARK 3 S11: 0.3686 S12: -0.4665 S13: 0.5511 REMARK 3 S21: 0.0510 S22: -0.2786 S23: -0.4752 REMARK 3 S31: -0.1673 S32: 0.7679 S33: -0.0927 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 318 THROUGH 347 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.2857 10.1108 -3.0239 REMARK 3 T TENSOR REMARK 3 T11: 0.1376 T22: 0.1354 REMARK 3 T33: 0.1310 T12: 0.0199 REMARK 3 T13: -0.0177 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 2.8376 L22: 1.3358 REMARK 3 L33: 3.2263 L12: -0.4378 REMARK 3 L13: -0.3556 L23: 0.7534 REMARK 3 S TENSOR REMARK 3 S11: 0.0908 S12: 0.2034 S13: -0.0502 REMARK 3 S21: -0.0547 S22: -0.0737 S23: 0.0458 REMARK 3 S31: 0.1386 S32: -0.0522 S33: -0.0412 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 8QML 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_1292133508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-23 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 : BM07 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951 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 : 129324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 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: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 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 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 25.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.58000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.58000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.61000 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 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 MET A -9 REMARK 465 TRP A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 PRO A -5 REMARK 465 GLN A -4 REMARK 465 PHE A -3 REMARK 465 GLU A -2 REMARK 465 LYS A -1 REMARK 465 ALA A 0 REMARK 465 SER A 1 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 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 LYS A 9 CE NZ REMARK 470 ARG A 12 CZ NH1 NH2 REMARK 470 ARG A 13 NH1 NH2 REMARK 470 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 37 CE NZ REMARK 470 LYS A 77 CD CE NZ REMARK 470 LYS A 80 CD CE NZ REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 LYS A 242 CE NZ REMARK 470 LYS A 243 CD CE NZ REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 LYS A 315 CG CD CE NZ REMARK 470 LYS A 333 CD CE NZ REMARK 470 ARG A 336 CD NE CZ NH1 NH2 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 785 O HOH A 791 2.10 REMARK 500 O HOH A 715 O HOH A 719 2.10 REMARK 500 O HOH A 519 O HOH A 589 2.10 REMARK 500 O HOH A 515 O HOH A 720 2.13 REMARK 500 O HOH A 647 O HOH A 769 2.15 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 750 O HOH A 803 2654 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 337 CB - CG - OD1 ANGL. DEV. = 6.2 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 PHE A 15 54.60 -93.24 REMARK 500 ASN A 78 45.09 -90.54 REMARK 500 ASN A 78 46.39 -91.59 REMARK 500 GLU A 161 -60.29 73.33 REMARK 500 THR A 175 -152.24 -151.53 REMARK 500 ALA A 196 -149.28 -119.80 REMARK 500 ASN A 288 12.49 -140.33 REMARK 500 LYS A 309 91.97 57.20 REMARK 500 SER A 311 -4.47 67.80 REMARK 500 ASP A 337 -156.65 -136.13 REMARK 500 GLU A 346 -150.47 -119.20 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 A 819 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 820 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 821 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A 822 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A 823 DISTANCE = 7.30 ANGSTROMS REMARK 525 HOH A 824 DISTANCE = 8.16 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 405 REMARK 610 CPS A 406 REMARK 610 CPS A 407 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 408 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 SF4 A 408 S1 105.1 REMARK 620 3 SF4 A 408 S3 117.1 105.1 REMARK 620 4 SF4 A 408 S4 118.6 103.5 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 408 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 SF4 A 408 S1 119.4 REMARK 620 3 SF4 A 408 S2 116.1 103.2 REMARK 620 4 SF4 A 408 S4 107.4 104.2 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 408 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 70 SG REMARK 620 2 SF4 A 408 S2 110.5 REMARK 620 3 SF4 A 408 S3 120.0 104.7 REMARK 620 4 SF4 A 408 S4 110.0 105.7 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 408 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAH A 401 N REMARK 620 2 SF4 A 408 S1 98.6 REMARK 620 3 SF4 A 408 S2 157.2 100.2 REMARK 620 4 SF4 A 408 S3 87.1 101.7 101.5 REMARK 620 5 SAH A 401 O 73.6 95.3 91.9 156.0 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8QMK RELATED DB: PDB REMARK 900 8QMK CONTAINS THE NATURAL SUBSTRATE DBREF 8QML A 2 348 UNP Q9X0Z6 HYDE_THEMA 2 348 SEQADV 8QML MET A -9 UNP Q9X0Z6 INITIATING METHIONINE SEQADV 8QML TRP A -8 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML SER A -7 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML HIS A -6 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML PRO A -5 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML GLN A -4 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML PHE A -3 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML GLU A -2 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML LYS A -1 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML ALA A 0 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML SER A 1 UNP Q9X0Z6 EXPRESSION TAG SEQADV 8QML OTY A 114 UNP Q9X0Z6 TYR 114 MODIFIED RESIDUE SEQADV 8QML SER A 311 UNP Q9X0Z6 CYS 311 ENGINEERED MUTATION SEQADV 8QML SER A 319 UNP Q9X0Z6 CYS 319 ENGINEERED MUTATION SEQADV 8QML 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 OTY 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 MET 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 OTY A 114 22 HET SAH A 401 30 HET 41K A 402 12 HET CPS A 403 42 HET CPS A 404 42 HET CPS A 405 29 HET CPS A 406 50 HET CPS A 407 50 HET SF4 A 408 8 HET CL A 409 1 HET SO4 A 410 5 HETNAM OTY 2-HYDROXY-L-TYROSINE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM 41K (2R,4R)-2-METHYL-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC ACID HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETSYN CPS CHAPS FORMUL 1 OTY C9 H11 N O4 FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 41K C6 H9 N O4 S FORMUL 4 CPS 5(C32 H58 N2 O7 S) FORMUL 9 SF4 FE4 S4 FORMUL 10 CL CL 1- FORMUL 11 SO4 O4 S 2- FORMUL 12 HOH *324(H2 O) HELIX 1 AA1 THR A 2 ARG A 12 1 11 HELIX 2 AA2 THR A 16 ILE A 26 1 11 HELIX 3 AA3 ASP A 28 GLY A 48 1 21 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 ALA A 151 1 11 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 PRO A 229 0 SHEET 2 AA1 7 GLU A 193 VAL A 200 1 N ALA A 196 O GLY A 226 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 ILE A 104 O THR A 134 SHEET 6 AA1 7 GLU A 50 SER A 60 1 N ALA A 55 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 PRO A 229 0 SHEET 2 AA2 7 GLU A 193 VAL A 200 1 N ALA A 196 O GLY A 226 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 ILE A 104 O THR A 134 SHEET 6 AA2 7 GLU A 50 SER A 60 1 N ALA A 55 O VAL A 105 SHEET 7 AA2 7 LYS A 333 PRO A 334 1 O LYS A 333 N VAL A 51 LINK C TYR A 113 N OTY A 114 1555 1555 1.33 LINK C OTY A 114 N MET A 115 1555 1555 1.34 LINK CB AASP A 316 C31ACPS A 404 1555 4455 1.50 LINK SG CYS A 63 FE2 SF4 A 408 1555 1555 2.23 LINK SG CYS A 67 FE3 SF4 A 408 1555 1555 2.32 LINK SG CYS A 70 FE1 SF4 A 408 1555 1555 2.20 LINK N SAH A 401 FE4 SF4 A 408 1555 1555 2.31 LINK O SAH A 401 FE4 SF4 A 408 1555 1555 2.24 CISPEP 1 MET A 115 PRO A 116 0 -2.36 CISPEP 2 SER A 297 PRO A 298 0 5.62 CRYST1 50.480 79.220 85.160 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 0.019810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011743 0.00000