HEADER LYASE 23-JUL-22 7YKN TITLE CRYSTAL STRUCTURE OF (6-4) PHOTOLYASE FROM VIBRIO CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRYPTOCHROME/PHOTOLYASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA PHOTOLYASE,(6-4) PHOTOLYASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: D6U24_03430, ERS013165_01011, ERS013186_03677, SOURCE 5 ERS013198_00016, ERS013199_00375, ERS013202_01140, ERS013207_00426; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOTOLYASE, DNA REPAIR, DMRL, [4FE-4S] CLUSTER, FAD, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR B.CAKILKAYA,I.H.KAVAKLI,H.DEMIRCI REVDAT 3 29-NOV-23 7YKN 1 REMARK REVDAT 2 29-MAR-23 7YKN 1 JRNL REVDAT 1 21-DEC-22 7YKN 0 JRNL AUTH B.CAKILKAYA,I.H.KAVAKLI,H.DEMIRCI JRNL TITL THE CRYSTAL STRUCTURE OF VIBRIO CHOLERAE (6-4) PHOTOLYASE JRNL TITL 2 REVEALS INTERACTIONS WITH COFACTORS AND A DNA-BINDING JRNL TITL 3 REGION. JRNL REF J.BIOL.CHEM. V. 299 02794 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36528063 JRNL DOI 10.1016/J.JBC.2022.102794 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.340 REMARK 3 FREE R VALUE TEST SET COUNT : 1068 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 24.6200 - 4.9900 1.00 4103 142 0.1826 0.2075 REMARK 3 2 4.9900 - 3.9600 1.00 3910 135 0.1617 0.1796 REMARK 3 3 3.9600 - 3.4600 0.99 3810 131 0.2594 0.3921 REMARK 3 4 3.4600 - 3.1500 1.00 3858 133 0.2293 0.2864 REMARK 3 5 3.1500 - 2.9200 1.00 3823 132 0.2270 0.2960 REMARK 3 6 2.9200 - 2.7500 1.00 3785 131 0.2454 0.2795 REMARK 3 7 2.7500 - 2.6100 1.00 3834 132 0.2768 0.3725 REMARK 3 8 2.6100 - 2.5000 1.00 3779 132 0.2887 0.3505 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.46 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 : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): -58.5743 40.7956 -1.8303 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.1209 REMARK 3 T33: 0.1644 T12: -0.1052 REMARK 3 T13: 0.0078 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.4235 L22: 2.2029 REMARK 3 L33: 0.7126 L12: 1.0558 REMARK 3 L13: -0.4673 L23: 0.2074 REMARK 3 S TENSOR REMARK 3 S11: -0.0543 S12: -0.0641 S13: -0.1502 REMARK 3 S21: 0.0573 S22: 0.0237 S23: -0.1815 REMARK 3 S31: -0.4381 S32: 0.1904 S33: 0.0589 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): -58.5945 42.3785 -5.0368 REMARK 3 T TENSOR REMARK 3 T11: 0.1911 T22: 0.1651 REMARK 3 T33: 0.1923 T12: -0.0846 REMARK 3 T13: 0.0190 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.7802 L22: 0.7598 REMARK 3 L33: 0.6288 L12: 0.1475 REMARK 3 L13: -0.0249 L23: 0.0958 REMARK 3 S TENSOR REMARK 3 S11: -0.0453 S12: 0.0996 S13: 0.1865 REMARK 3 S21: -0.1906 S22: 0.1240 S23: -0.0393 REMARK 3 S31: -0.2815 S32: 0.2987 S33: -0.0519 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -62.4626 14.7188 -15.8401 REMARK 3 T TENSOR REMARK 3 T11: 0.2319 T22: 0.1469 REMARK 3 T33: 0.2493 T12: -0.0136 REMARK 3 T13: 0.0844 T23: -0.0587 REMARK 3 L TENSOR REMARK 3 L11: 1.9400 L22: 4.9897 REMARK 3 L33: 1.2104 L12: 0.3609 REMARK 3 L13: 0.8393 L23: -1.8865 REMARK 3 S TENSOR REMARK 3 S11: -0.2156 S12: 0.3847 S13: -0.2898 REMARK 3 S21: -0.5327 S22: 0.1877 S23: -0.3454 REMARK 3 S31: 0.3139 S32: 0.3074 S33: -0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): -78.0956 20.2061 0.4475 REMARK 3 T TENSOR REMARK 3 T11: 0.1071 T22: 0.0390 REMARK 3 T33: 0.1709 T12: -0.0110 REMARK 3 T13: -0.0508 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.0310 L22: 0.7851 REMARK 3 L33: 0.7306 L12: 0.6210 REMARK 3 L13: -0.0782 L23: -0.1140 REMARK 3 S TENSOR REMARK 3 S11: -0.1227 S12: -0.1135 S13: -0.1341 REMARK 3 S21: -0.1496 S22: 0.0773 S23: 0.4251 REMARK 3 S31: 0.0174 S32: 0.1075 S33: 0.0334 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 266 ) REMARK 3 ORIGIN FOR THE GROUP (A): -80.7193 26.7243 3.1789 REMARK 3 T TENSOR REMARK 3 T11: 0.1157 T22: 0.0619 REMARK 3 T33: 0.1602 T12: -0.0234 REMARK 3 T13: -0.0201 T23: -0.0149 REMARK 3 L TENSOR REMARK 3 L11: 1.0747 L22: 0.3649 REMARK 3 L33: 0.9068 L12: 0.6419 REMARK 3 L13: -0.3433 L23: -0.1440 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: 0.0620 S13: 0.0855 REMARK 3 S21: -0.0672 S22: -0.0263 S23: 0.2202 REMARK 3 S31: 0.0123 S32: 0.0193 S33: 0.0090 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 267 THROUGH 368 ) REMARK 3 ORIGIN FOR THE GROUP (A): -76.7395 23.7404 -8.1268 REMARK 3 T TENSOR REMARK 3 T11: 0.1554 T22: 0.0542 REMARK 3 T33: 0.1292 T12: -0.0349 REMARK 3 T13: -0.0097 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.1947 L22: 0.4572 REMARK 3 L33: 0.5948 L12: -0.1370 REMARK 3 L13: 0.2088 L23: -0.0474 REMARK 3 S TENSOR REMARK 3 S11: -0.0695 S12: 0.0405 S13: 0.0322 REMARK 3 S21: -0.0885 S22: 0.0444 S23: -0.0153 REMARK 3 S31: -0.0193 S32: -0.0716 S33: 0.0266 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 369 THROUGH 461 ) REMARK 3 ORIGIN FOR THE GROUP (A): -86.1120 24.6351 -15.7801 REMARK 3 T TENSOR REMARK 3 T11: 0.1326 T22: 0.1126 REMARK 3 T33: 0.0922 T12: 0.0087 REMARK 3 T13: -0.0269 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 2.9469 L22: 1.5212 REMARK 3 L33: 1.1105 L12: 0.8773 REMARK 3 L13: 0.1229 L23: 0.1497 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: 0.1608 S13: -0.1425 REMARK 3 S21: -0.1734 S22: -0.0038 S23: 0.0111 REMARK 3 S31: -0.0763 S32: -0.1270 S33: -0.0025 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 462 THROUGH 516 ) REMARK 3 ORIGIN FOR THE GROUP (A): -96.2386 19.2665 -28.4323 REMARK 3 T TENSOR REMARK 3 T11: 0.2121 T22: 0.3386 REMARK 3 T33: 0.0976 T12: -0.0448 REMARK 3 T13: -0.0395 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 3.0862 L22: 3.3301 REMARK 3 L33: 5.4656 L12: 0.9045 REMARK 3 L13: 0.5485 L23: 1.0344 REMARK 3 S TENSOR REMARK 3 S11: -0.2817 S12: 0.6986 S13: -0.1287 REMARK 3 S21: -0.3184 S22: 0.2051 S23: 0.0116 REMARK 3 S31: 0.0951 S32: 0.1561 S33: 0.0597 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 7YKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300031074. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32043 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 24.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 60.40 REMARK 200 R MERGE (I) : 1.38200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 3.76500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 4DJA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5%(V/V) PEG400, 2 M AMMONIUM REMARK 280 CITRATE/CITRIC ACID PH 7.5, 1 M SODIUM SULFATE DECAHYDRATE, REMARK 280 MICROBATCH, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.67433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.34867 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.67433 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.34867 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.67433 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 51.34867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.67433 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 51.34867 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: 1600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 478 REMARK 465 ALA A 479 REMARK 465 ASN A 480 REMARK 465 ASN A 481 REMARK 465 PRO A 482 REMARK 465 ARG A 483 REMARK 465 ILE A 484 REMARK 465 GLY A 485 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 LEU A 14 53.11 -90.46 REMARK 500 ILE A 246 -50.33 -121.74 REMARK 500 LEU A 268 -128.31 58.40 REMARK 500 VAL A 379 -68.30 -120.55 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 A1231 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1232 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1233 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1234 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A1235 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A1236 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1237 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1238 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A1239 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A1240 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A1241 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A1242 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A1243 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A1244 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A1245 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A1246 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A1247 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A1248 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A1249 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A1250 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A1251 DISTANCE = 7.36 ANGSTROMS REMARK 525 HOH A1252 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH A1253 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH A1254 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A1255 DISTANCE = 7.84 ANGSTROMS REMARK 525 HOH A1256 DISTANCE = 8.17 ANGSTROMS REMARK 525 HOH A1257 DISTANCE = 9.74 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 606 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 357 SG REMARK 620 2 SF4 A 606 S1 115.1 REMARK 620 3 SF4 A 606 S2 108.0 104.2 REMARK 620 4 SF4 A 606 S4 119.9 104.0 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 606 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 445 SG REMARK 620 2 SF4 A 606 S2 122.2 REMARK 620 3 SF4 A 606 S3 107.7 104.2 REMARK 620 4 SF4 A 606 S4 112.9 104.0 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 606 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 448 SG REMARK 620 2 SF4 A 606 S1 113.2 REMARK 620 3 SF4 A 606 S2 112.8 104.1 REMARK 620 4 SF4 A 606 S3 116.9 104.3 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 606 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 461 SG REMARK 620 2 SF4 A 606 S1 118.3 REMARK 620 3 SF4 A 606 S3 118.7 104.1 REMARK 620 4 SF4 A 606 S4 105.7 104.2 104.2 REMARK 620 N 1 2 3 DBREF1 7YKN A 1 516 UNP A0A2V4NVF4_VIBCL DBREF2 7YKN A A0A2V4NVF4 1 516 SEQADV 7YKN MET A -19 UNP A0A2V4NVF INITIATING METHIONINE SEQADV 7YKN GLY A -18 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN SER A -17 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN SER A -16 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A -15 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A -14 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A -13 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A -12 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A -11 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A -10 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN SER A -9 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN SER A -8 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN GLY A -7 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN LEU A -6 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN VAL A -5 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN PRO A -4 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN ARG A -3 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN GLY A -2 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN SER A -1 UNP A0A2V4NVF EXPRESSION TAG SEQADV 7YKN HIS A 0 UNP A0A2V4NVF EXPRESSION TAG SEQRES 1 A 536 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 536 LEU VAL PRO ARG GLY SER HIS MET ARG TYR SER VAL VAL SEQRES 3 A 536 ARG LEU ILE LEU GLY ASP GLN LEU ASN HIS ALA HIS SER SEQRES 4 A 536 TRP PHE SER GLU HIS ARG ASP ASP VAL LEU TYR LEU ILE SEQRES 5 A 536 ALA GLU LEU HIS GLN GLU GLN GLU TYR VAL ARG HIS HIS SEQRES 6 A 536 ILE GLN LYS GLN CYS ALA PHE PHE ALA ALA MET GLN ALA SEQRES 7 A 536 PHE ALA ASP TYR LEU SER ALA GLU GLY HIS HIS VAL TRP SEQRES 8 A 536 HIS LEU ASP LEU ASP ALA SER ALA GLN TYR ASN ASP LEU SEQRES 9 A 536 PRO ASP LEU ILE ALA GLN ILE CYS GLN GLN VAL GLN ALA SEQRES 10 A 536 ASP ALA PHE GLN TYR GLN ARG PRO ASP GLU TYR ARG LEU SEQRES 11 A 536 LEU GLU GLN MET ALA ASN LEU ARG LEU SER GLY ILE THR SEQRES 12 A 536 ILE GLY CYS VAL ASP THR GLU HIS PHE LEU LEU PRO PHE SEQRES 13 A 536 ALA GLU ILE PRO GLU GLN PHE PRO ALA SER LYS ALA VAL SEQRES 14 A 536 LEU MET GLU HIS PHE TYR ARG ARG MET ARG LYS ARG PHE SEQRES 15 A 536 GLY TYR LEU MET THR ALA ASP GLY LYS PRO GLU GLY GLY SEQRES 16 A 536 GLN TRP ASN PHE ASP ALA ASP ASN ARG ASN LYS LEU LYS SEQRES 17 A 536 SER PRO ASP LEU LEU GLN LEU PRO THR PRO LEU CYS PHE SEQRES 18 A 536 ASP ASN PRO VAL ALA SER ILE LYS ALA ARG ILE GLU ARG SEQRES 19 A 536 HIS ARG ILE PRO SER ILE GLY GLN VAL GLY GLU SER LEU SEQRES 20 A 536 LEU TRP PRO ILE ASN ARG ALA GLN ALA LEU SER LEU LEU SEQRES 21 A 536 ALA HIS PHE CYS GLN ILE CYS LEU PRO ASN PHE GLY ARG SEQRES 22 A 536 PHE GLN ASP ALA MET THR ALA GLN HIS PRO HIS ARG TRP SEQRES 23 A 536 SER LEU TYR HIS SER ARG LEU SER PHE ALA LEU ASN SER SEQRES 24 A 536 LYS LEU LEU SER PRO ARG GLU VAL ILE GLU ALA THR ILE SEQRES 25 A 536 SER ALA TYR ARG ALA ALA GLN GLY GLN ILE SER LEU ALA SEQRES 26 A 536 GLN VAL GLU GLY PHE VAL ARG GLN ILE LEU GLY TRP ARG SEQRES 27 A 536 GLU TYR VAL ARG GLY MET TYR TRP SER ASN MET PRO HIS SEQRES 28 A 536 TYR GLN THR ARG ASN HIS LEU GLY ALA GLN ARG PRO LEU SEQRES 29 A 536 PRO SER TYR PHE TRP ASN GLY GLN THR LYS MET ARG CYS SEQRES 30 A 536 LEU GLN GLN ALA ILE THR GLN SER LEU ASP PHE GLY TYR SEQRES 31 A 536 ALA HIS HIS ILE GLN ARG LEU MET VAL THR GLY ASN PHE SEQRES 32 A 536 ALA LEU LEU THR GLU CYS ASP PRO ASP GLN VAL ASP ALA SEQRES 33 A 536 TRP TYR LEU GLY ILE TYR ILE ASP ALA ILE GLU TRP VAL SEQRES 34 A 536 GLU LEU PRO ASN THR ARG GLY MET ALA LEU PHE ALA ASP SEQRES 35 A 536 GLY GLY LEU ILE ALA THR LYS PRO TYR SER ALA SER GLY SEQRES 36 A 536 SER TYR ILE ASN LYS MET SER ASP TYR CYS ALA SER CYS SEQRES 37 A 536 ALA TYR GLN VAL LYS LEU LYS SER GLY GLU LYS ALA CYS SEQRES 38 A 536 PRO LEU ASN SER LEU TYR TRP ARG PHE MET LEU LYS HIS SEQRES 39 A 536 ARG ASP ARG LEU ALA ASN ASN PRO ARG ILE GLY MET LEU SEQRES 40 A 536 TYR LYS THR TRP ASP LYS MET THR SER ASP SER GLN GLN SEQRES 41 A 536 ALA ILE LEU SER THR ALA ASP ALA TYR LEU SER GLN ILE SEQRES 42 A 536 GLU SER LEU HET GOL A 601 6 HET GOL A 602 6 HET DLZ A 603 23 HET FAD A 604 53 HET IMD A 605 5 HET SF4 A 606 8 HETNAM GOL GLYCEROL HETNAM DLZ 1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-3,4-DIHYDROPTERIDIN- HETNAM 2 DLZ 8(2H)-YL)-D-RIBITOL HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM IMD IMIDAZOLE HETNAM SF4 IRON/SULFUR CLUSTER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN DLZ 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 DLZ C13 H18 N4 O6 FORMUL 5 FAD C27 H33 N9 O15 P2 FORMUL 6 IMD C3 H5 N2 1+ FORMUL 7 SF4 FE4 S4 FORMUL 8 HOH *557(H2 O) HELIX 1 AA1 LEU A 35 TYR A 41 1 7 HELIX 2 AA2 HIS A 45 GLU A 66 1 22 HELIX 3 AA3 ASP A 74 ALA A 79 1 6 HELIX 4 AA4 ASP A 83 GLN A 96 1 14 HELIX 5 AA5 GLU A 107 LEU A 117 1 11 HELIX 6 AA6 PRO A 135 ALA A 137 5 3 HELIX 7 AA7 GLU A 138 PHE A 143 1 6 HELIX 8 AA8 LEU A 150 GLY A 163 1 14 HELIX 9 AA9 PHE A 179 ASN A 183 5 5 HELIX 10 AB1 LYS A 188 GLN A 194 1 7 HELIX 11 AB2 VAL A 205 HIS A 215 1 11 HELIX 12 AB3 ASN A 232 CYS A 247 1 16 HELIX 13 AB4 CYS A 247 GLY A 252 1 6 HELIX 14 AB5 LEU A 273 SER A 279 1 7 HELIX 15 AB6 SER A 283 ALA A 298 1 16 HELIX 16 AB7 SER A 303 GLY A 316 1 14 HELIX 17 AB8 GLY A 316 GLN A 333 1 18 HELIX 18 AB9 PRO A 345 ASN A 350 5 6 HELIX 19 AC1 MET A 355 GLY A 369 1 15 HELIX 20 AC2 HIS A 372 VAL A 379 1 8 HELIX 21 AC3 VAL A 379 THR A 387 1 9 HELIX 22 AC4 ASP A 390 TYR A 402 1 13 HELIX 23 AC5 ILE A 406 GLY A 416 1 11 HELIX 24 AC6 SER A 434 SER A 442 1 9 HELIX 25 AC7 ASP A 443 CYS A 448 1 6 HELIX 26 AC8 CYS A 461 HIS A 474 1 14 HELIX 27 AC9 LEU A 487 LYS A 493 1 7 HELIX 28 AD1 THR A 495 GLN A 512 1 18 HELIX 29 AD2 ILE A 513 LEU A 516 5 4 SHEET 1 AA1 5 HIS A 69 LEU A 73 0 SHEET 2 AA1 5 VAL A 28 ALA A 33 1 N TYR A 30 O HIS A 69 SHEET 3 AA1 5 VAL A 5 LEU A 8 1 N ARG A 7 O LEU A 29 SHEET 4 AA1 5 ALA A 99 GLN A 103 1 O ALA A 99 N VAL A 6 SHEET 5 AA1 5 THR A 123 VAL A 127 1 O THR A 123 N PHE A 100 SHEET 1 AA2 2 ASN A 203 PRO A 204 0 SHEET 2 AA2 2 SER A 226 LEU A 227 -1 O LEU A 227 N ASN A 203 LINK SG CYS A 357 FE3 SF4 A 606 1555 1555 2.27 LINK SG CYS A 445 FE1 SF4 A 606 1555 1555 2.28 LINK SG CYS A 448 FE4 SF4 A 606 1555 1555 2.26 LINK SG CYS A 461 FE2 SF4 A 606 1555 1555 2.26 CRYST1 200.751 200.751 77.023 90.00 90.00 120.00 P 64 2 2 12 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 0.004981 0.002876 0.000000 0.00000 SCALE2 0.000000 0.005752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012983 0.00000