HEADER TRANSCRIPTION/DNA/TRANSFERASE 23-MAY-22 8CYF TITLE WHIB3 BOUND TO SIGMAAR4-RNAP BETA FLAP TIP CHIMERA AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDOX- AND PH-RESPONSIVE TRANSCRIPTIONAL REGULATOR WHIB3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: FULL WHIB3 SEQUENCE WAS USED FOR CRYSTALLIZATION, THE COMPND 6 N- AND C- TERMINAL RESIDUES ARE NOT VISIBLE DUE TO FLEXIBILITY.; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA POLYMERASE SIGMA FACTOR, DNA-DIRECTED RNA POLYMERASE COMPND 9 SUBUNIT BETA CHIMERA,DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: RNAP SUBUNIT BETA,RNA POLYMERASE SUBUNIT BETA,TRANSCRIPTASE COMPND 12 SUBUNIT BETA; COMPND 13 EC: 2.7.7.6; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: THE LAST 82 RESIDUES IN THE C-TERMINAL OF THE PRIMARY COMPND 16 SIGMA FACTOR WAS FUSED WITH THE FLAP TIP HELIX (T815-A829) FROM RNA COMPND 17 POLYMERASE BETA SUBUNIT, WITH SIX HISTIDINE TAG IN THE N-TERMINAL,THE COMPND 18 LAST 82 RESIDUES IN THE C-TERMINAL OF THE PRIMARY SIGMA FACTOR WAS COMPND 19 FUSED WITH THE FLAP TIP HELIX (T815-A829) FROM RNA POLYMERASE BETA COMPND 20 SUBUNIT, WITH SIX HISTIDINE TAG IN THE N-TERMINAL; COMPND 21 MOL_ID: 3; COMPND 22 MOLECULE: DNA (5'-D(*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)- COMPND 23 3'); COMPND 24 CHAIN: C; COMPND 25 ENGINEERED: YES; COMPND 26 OTHER_DETAILS: DNA SEQUENCE FROM WHIB7 PROMOTER; COMPND 27 MOL_ID: 4; COMPND 28 MOLECULE: DNA (5'-D(*CP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*T)- COMPND 29 3'); COMPND 30 CHAIN: D; COMPND 31 ENGINEERED: YES; COMPND 32 OTHER_DETAILS: DNA SEQUENCE FROM WHIB7 PROMOTER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: WHIB3, RV3416; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 10 ORGANISM_TAXID: 1773; SOURCE 11 GENE: SIGA, ERS007670_01286, ERS007681_03833, ERS007688_01862; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 17 ORGANISM_TAXID: 1773; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 21 ORGANISM_TAXID: 1773 KEYWDS REDOX SENSOR, TRANSCRIPTIONAL FACTOR, PROTEIN-DNA COMPLEX, KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION-DNA-TRANSFERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.WAN,L.M.ZHANG REVDAT 4 25-OCT-23 8CYF 1 REMARK REVDAT 3 14-JUN-23 8CYF 1 JRNL REVDAT 2 07-JUN-23 8CYF 1 REMARK REVDAT 1 17-MAY-23 8CYF 0 JRNL AUTH T.WAN,M.HOROVA,V.KHETRAPAL,S.LI,C.JONES,A.SCHACHT,X.SUN, JRNL AUTH 2 L.ZHANG JRNL TITL STRUCTURAL BASIS OF DNA BINDING BY THE WHIB-LIKE JRNL TITL 2 TRANSCRIPTION FACTOR WHIB3 IN MYCOBACTERIUM TUBERCULOSIS. JRNL REF J.BIOL.CHEM. V. 299 04777 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37142222 JRNL DOI 10.1016/J.JBC.2023.104777 REMARK 2 REMARK 2 RESOLUTION. 2.44 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 13476 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 673 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 38.1500 - 4.1800 0.99 2695 140 0.1910 0.2233 REMARK 3 2 4.1800 - 3.3200 1.00 2607 119 0.2150 0.2384 REMARK 3 3 3.3200 - 2.9000 1.00 2556 142 0.2672 0.2863 REMARK 3 4 2.9000 - 2.6300 1.00 2514 155 0.2798 0.3025 REMARK 3 5 2.6300 - 2.4400 0.96 2431 117 0.3850 0.4256 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) : 0.395 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.046 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.27 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 : 0.018 2069 REMARK 3 ANGLE : 2.228 2924 REMARK 3 CHIRALITY : 0.213 321 REMARK 3 PLANARITY : 0.012 268 REMARK 3 DIHEDRAL : 27.048 833 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 16 THROUGH 90) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1303 25.0650 28.9010 REMARK 3 T TENSOR REMARK 3 T11: 0.4404 T22: 0.3527 REMARK 3 T33: 0.4385 T12: 0.0257 REMARK 3 T13: 0.0393 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 7.9744 L22: 6.4356 REMARK 3 L33: 6.1985 L12: 1.8755 REMARK 3 L13: 0.9638 L23: 0.4684 REMARK 3 S TENSOR REMARK 3 S11: 0.1819 S12: -0.5567 S13: -0.1531 REMARK 3 S21: 0.2657 S22: -0.2042 S23: 0.2970 REMARK 3 S31: 0.0267 S32: -0.2853 S33: -0.0100 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 450 THROUGH 546) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2184 42.7811 18.2608 REMARK 3 T TENSOR REMARK 3 T11: 0.5524 T22: 0.5034 REMARK 3 T33: 0.6484 T12: 0.1191 REMARK 3 T13: 0.0647 T23: 0.0997 REMARK 3 L TENSOR REMARK 3 L11: 4.0767 L22: 5.2750 REMARK 3 L33: 2.7565 L12: 1.4956 REMARK 3 L13: 0.3968 L23: 0.0270 REMARK 3 S TENSOR REMARK 3 S11: 0.1323 S12: 0.0027 S13: 0.8155 REMARK 3 S21: 0.0015 S22: 0.1045 S23: 0.8563 REMARK 3 S31: -0.4486 S32: -0.5955 S33: -0.1859 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 16) REMARK 3 ORIGIN FOR THE GROUP (A): 40.1680 31.2225 33.4166 REMARK 3 T TENSOR REMARK 3 T11: 0.5885 T22: 0.7837 REMARK 3 T33: 0.6128 T12: -0.0671 REMARK 3 T13: -0.1171 T23: 0.0297 REMARK 3 L TENSOR REMARK 3 L11: 1.6161 L22: 3.8637 REMARK 3 L33: 3.0944 L12: -1.5488 REMARK 3 L13: -0.4519 L23: -2.2366 REMARK 3 S TENSOR REMARK 3 S11: 0.2691 S12: -0.1567 S13: -0.3212 REMARK 3 S21: 0.2707 S22: -0.2359 S23: -0.0928 REMARK 3 S31: -0.4048 S32: -0.7343 S33: -0.0504 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 16) REMARK 3 ORIGIN FOR THE GROUP (A): 41.4800 34.2592 35.3907 REMARK 3 T TENSOR REMARK 3 T11: 0.6368 T22: 1.0409 REMARK 3 T33: 0.6722 T12: -0.0011 REMARK 3 T13: -0.0950 T23: 0.0253 REMARK 3 L TENSOR REMARK 3 L11: 1.9543 L22: 5.0798 REMARK 3 L33: 3.9717 L12: -1.2025 REMARK 3 L13: 1.7086 L23: 0.5729 REMARK 3 S TENSOR REMARK 3 S11: 0.1723 S12: -0.5205 S13: -0.3747 REMARK 3 S21: 0.8546 S22: 0.3442 S23: -0.2226 REMARK 3 S31: 0.2642 S32: 0.9268 S33: -0.5401 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 8CYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13547 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 15.30 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.20.1_4487 REMARK 200 STARTING MODEL: 8CWR REMARK 200 REMARK 200 REMARK: LARGE DIAMOND-SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CA(AC)2, 0.1 M NA CACODYLATE, PH REMARK 280 6.5, 10%~13% PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 25.34850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.69000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.46700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.69000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.34850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.46700 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 1 REMARK 465 PRO A 2 REMARK 465 GLN A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 5 REMARK 465 GLN A 6 REMARK 465 LEU A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 9 REMARK 465 PRO A 10 REMARK 465 ASN A 11 REMARK 465 ALA A 12 REMARK 465 ASP A 13 REMARK 465 ILE A 14 REMARK 465 TRP A 15 REMARK 465 THR A 91 REMARK 465 MET A 92 REMARK 465 GLY A 93 REMARK 465 ARG A 94 REMARK 465 THR A 95 REMARK 465 ARG A 96 REMARK 465 GLY A 97 REMARK 465 ILE A 98 REMARK 465 ARG A 99 REMARK 465 ARG A 100 REMARK 465 THR A 101 REMARK 465 ALA A 102 REMARK 465 MET B 438 REMARK 465 ALA B 439 REMARK 465 HIS B 440 REMARK 465 HIS B 441 REMARK 465 HIS B 442 REMARK 465 HIS B 443 REMARK 465 HIS B 444 REMARK 465 HIS B 445 REMARK 465 VAL B 446 REMARK 465 ALA B 447 REMARK 465 VAL B 448 REMARK 465 ASP B 449 REMARK 465 TYR B 526 REMARK 465 LEU B 527 REMARK 465 ASP B 528 REMARK 465 GLY B 529 REMARK 465 SER B 530 REMARK 465 SER B 531 REMARK 465 GLY B 532 REMARK 465 SER B 533 REMARK 465 GLU B 547 REMARK 465 LYS B 548 REMARK 465 ALA B 549 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 DA C 5 O5' - P - OP2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT C 6 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG C 14 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC D 10 O5' - P - OP2 ANGL. DEV. = -7.1 DEGREES REMARK 500 DC D 10 O5' - C5' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG D 11 O5' - P - OP2 ANGL. DEV. = -7.9 DEGREES REMARK 500 DT D 13 O5' - P - OP1 ANGL. DEV. = -11.1 DEGREES REMARK 500 DT D 13 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT D 15 O5' - P - OP2 ANGL. DEV. = -10.2 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 GLU A 71 107.89 -40.46 REMARK 500 LYS A 89 129.53 -37.36 REMARK 500 ARG B 519 51.95 -153.12 REMARK 500 GLN B 521 38.66 -86.50 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 SF4 A 200 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 SF4 A 200 S1 120.2 REMARK 620 3 SF4 A 200 S2 120.7 96.1 REMARK 620 4 SF4 A 200 S3 116.4 100.3 98.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 200 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 53 SG REMARK 620 2 SF4 A 200 S2 119.9 REMARK 620 3 SF4 A 200 S3 120.9 102.9 REMARK 620 4 SF4 A 200 S4 108.0 98.8 103.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 200 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 56 SG REMARK 620 2 SF4 A 200 S1 120.1 REMARK 620 3 SF4 A 200 S3 110.4 103.1 REMARK 620 4 SF4 A 200 S4 123.7 95.7 100.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 200 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 SF4 A 200 S1 123.1 REMARK 620 3 SF4 A 200 S2 121.7 97.2 REMARK 620 4 SF4 A 200 S4 115.6 95.0 98.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8CWT RELATED DB: PDB REMARK 900 WHIB3 AND SIGA4 CRYSTAL STRUCTURE WITHOUT DNA IN P43212 SPACE GROUP REMARK 900 RELATED ID: 8CWR RELATED DB: PDB REMARK 900 WHIB3 AND SIGA4 CRYSTAL STRUCTURE WITHOUT DNA IN R3 SPACE GROUP DBREF 8CYF A 1 102 UNP P9WF41 WHIB3_MYCTU 1 102 DBREF1 8CYF B 446 528 UNP A0A654TMB9_MYCTX DBREF2 8CYF B A0A654TMB9 295 377 DBREF 8CYF B 535 549 UNP A1KGE7 RPOB_MYCBP 815 829 DBREF 8CYF C 1 16 PDB 8CYF 8CYF 1 16 DBREF 8CYF D 1 16 PDB 8CYF 8CYF 1 16 SEQADV 8CYF MET B 438 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF ALA B 439 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF HIS B 440 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF HIS B 441 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF HIS B 442 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF HIS B 443 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF HIS B 444 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF HIS B 445 UNP A0A654TMB EXPRESSION TAG SEQADV 8CYF GLY B 529 UNP A0A654TMB LINKER SEQADV 8CYF SER B 530 UNP A0A654TMB LINKER SEQADV 8CYF SER B 531 UNP A0A654TMB LINKER SEQADV 8CYF GLY B 532 UNP A0A654TMB LINKER SEQADV 8CYF SER B 533 UNP A0A654TMB LINKER SEQADV 8CYF GLY B 534 UNP A0A654TMB LINKER SEQRES 1 A 102 MET PRO GLN PRO GLU GLN LEU PRO GLY PRO ASN ALA ASP SEQRES 2 A 102 ILE TRP ASN TRP GLN LEU GLN GLY LEU CYS ARG GLY MET SEQRES 3 A 102 ASP SER SER MET PHE PHE HIS PRO ASP GLY GLU ARG GLY SEQRES 4 A 102 ARG ALA ARG THR GLN ARG GLU GLN ARG ALA LYS GLU MET SEQRES 5 A 102 CYS ARG ARG CYS PRO VAL ILE GLU ALA CYS ARG SER HIS SEQRES 6 A 102 ALA LEU GLU VAL GLY GLU PRO TYR GLY VAL TRP GLY GLY SEQRES 7 A 102 LEU SER GLU SER GLU ARG ASP LEU LEU LEU LYS GLY THR SEQRES 8 A 102 MET GLY ARG THR ARG GLY ILE ARG ARG THR ALA SEQRES 1 B 112 MET ALA HIS HIS HIS HIS HIS HIS VAL ALA VAL ASP ALA SEQRES 2 B 112 VAL SER PHE THR LEU LEU GLN ASP GLN LEU GLN SER VAL SEQRES 3 B 112 LEU ASP THR LEU SER GLU ARG GLU ALA GLY VAL VAL ARG SEQRES 4 B 112 LEU ARG PHE GLY LEU THR ASP GLY GLN PRO ARG THR LEU SEQRES 5 B 112 ASP GLU ILE GLY GLN VAL TYR GLY VAL THR ARG GLU ARG SEQRES 6 B 112 ILE ARG GLN ILE GLU SER LYS THR MET SER LYS LEU ARG SEQRES 7 B 112 HIS PRO SER ARG SER GLN VAL LEU ARG ASP TYR LEU ASP SEQRES 8 B 112 GLY SER SER GLY SER GLY THR PRO GLU GLU ARG LEU LEU SEQRES 9 B 112 ARG ALA ILE PHE GLY GLU LYS ALA SEQRES 1 C 16 DG DA DA DA DA DT DC DG DG DT DT DG DT SEQRES 2 C 16 DG DG DT SEQRES 1 D 16 DC DA DC DC DA DC DA DA DC DC DG DA DT SEQRES 2 D 16 DT DT DT HET SF4 A 200 8 HET CAC B 601 5 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CAC CACODYLATE ION HETSYN CAC DIMETHYLARSINATE FORMUL 5 SF4 FE4 S4 FORMUL 6 CAC C2 H6 AS O2 1- FORMUL 7 HOH *3(H2 O) HELIX 1 AA1 ASN A 16 GLY A 21 5 6 HELIX 2 AA2 ASP A 27 PHE A 31 5 5 HELIX 3 AA3 ARG A 38 ARG A 55 1 18 HELIX 4 AA4 VAL A 58 GLY A 70 1 13 HELIX 5 AA5 SER A 80 LYS A 89 1 10 HELIX 6 AA6 SER B 452 ASP B 465 1 14 HELIX 7 AA7 SER B 468 GLY B 480 1 13 HELIX 8 AA8 THR B 488 GLY B 497 1 10 HELIX 9 AA9 THR B 499 ARG B 515 1 17 HELIX 10 AB1 HIS B 516 SER B 520 5 5 HELIX 11 AB2 THR B 535 PHE B 545 1 11 LINK SG CYS A 23 FE4 SF4 A 200 1555 1555 2.27 LINK SG CYS A 53 FE1 SF4 A 200 1555 1555 2.30 LINK SG CYS A 56 FE2 SF4 A 200 1555 1555 2.37 LINK SG CYS A 62 FE3 SF4 A 200 1555 1555 2.23 CRYST1 50.697 72.934 95.380 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 0.019725 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010484 0.00000