HEADER STRUCTURAL PROTEIN 25-AUG-20 7CV0 TITLE CRYSTAL STRUCTURE OF B. HALODURANS NIAR IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR NIAR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS (STRAIN ATCC BAA-125 / DSM SOURCE 3 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 4 ORGANISM_TAXID: 272558; SOURCE 5 GENE: BH1216; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NIAR, TRANSCRIPTION FACTOR, TRANSCTION, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.LEE,D.W.LEE,Y.W.PARK,M.Y.LEE,K.H.JEONG REVDAT 2 29-NOV-23 7CV0 1 REMARK REVDAT 1 16-DEC-20 7CV0 0 JRNL AUTH D.W.LEE,Y.W.PARK,M.Y.LEE,K.H.JEONG,J.Y.LEE JRNL TITL STRUCTURAL ANALYSIS AND INSIGHT INTO EFFECTOR BINDING OF THE JRNL TITL 2 NIACIN-RESPONSIVE REPRESSOR NIAR FROM BACILLUS HALODURANS. JRNL REF SCI REP V. 10 21039 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 33273654 JRNL DOI 10.1038/S41598-020-78148-X REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 575 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 19.9260 - 3.1681 1.00 2955 142 0.1848 0.1966 REMARK 3 2 3.1681 - 2.5162 1.00 2738 154 0.2177 0.2642 REMARK 3 3 2.5162 - 2.1986 1.00 2717 138 0.2191 0.2621 REMARK 3 4 2.1986 - 1.9980 0.99 2656 141 0.2289 0.2553 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 1374 REMARK 3 ANGLE : 0.513 1859 REMARK 3 CHIRALITY : 0.041 224 REMARK 3 PLANARITY : 0.003 235 REMARK 3 DIHEDRAL : 16.494 845 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7CV0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-17 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 : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97941 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11730 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.998 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.2110 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.600 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: 1J5Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TACSIMATE, BIS-TRIS PH 6.5, PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 88.10150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.18250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.18250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 132.15225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.18250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.18250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.05075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.18250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.18250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 132.15225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.18250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.18250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.05075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.10150 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: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 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 LEU A 176 O HOH A 301 2.16 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 SER A 137 -155.36 -140.69 REMARK 500 LEU A 142 52.98 -95.59 REMARK 500 SER A 143 -165.65 -79.85 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 91 OE1 REMARK 620 2 GLU A 91 OE2 56.4 REMARK 620 3 HIS A 150 NE2 122.5 79.2 REMARK 620 4 HIS A 152 NE2 115.4 105.9 110.3 REMARK 620 5 HOH A 398 O 90.6 141.0 107.6 107.1 REMARK 620 N 1 2 3 4 DBREF 7CV0 A 1 179 UNP Q9KDJ7 Q9KDJ7_BACHD 1 179 SEQRES 1 A 179 MET SER ASP GLU LYS LYS ILE LEU GLY GLU GLU ARG ARG SEQRES 2 A 179 SER LEU LEU ILE LYS TRP LEU LYS ALA SER ASP THR PRO SEQRES 3 A 179 LEU THR GLY ALA GLU LEU ALA LYS ARG THR ASN VAL SER SEQRES 4 A 179 ARG GLN VAL ILE VAL GLN ASP VAL SER LEU LEU LYS ALA SEQRES 5 A 179 LYS ASN HIS PRO ILE LEU ALA THR ALA GLN GLY TYR ILE SEQRES 6 A 179 TYR MET LYS GLU ALA ASN THR VAL GLN ALA GLN ARG VAL SEQRES 7 A 179 VAL ALA CYS GLN HIS GLY PRO ALA ASP MET LYS ASP GLU SEQRES 8 A 179 LEU LEU THR LEU VAL ASP HIS GLY VAL LEU ILE LYS ASP SEQRES 9 A 179 VAL THR VAL ASP HIS PRO VAL TYR GLY ASP ILE THR ALA SEQRES 10 A 179 SER LEU HIS LEU LYS SER ARG LYS ASP VAL ALA LEU PHE SEQRES 11 A 179 CYS LYS ARG MET GLU GLU SER ASN GLY THR LEU LEU SER SEQRES 12 A 179 THR LEU THR LYS GLY VAL HIS MET HIS THR LEU GLU ALA SEQRES 13 A 179 GLU SER GLU ALA ILE LEU ASP GLU ALA ILE ARG ALA LEU SEQRES 14 A 179 GLU GLU LYS GLY TYR LEU LEU ASN SER PHE HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *129(H2 O) HELIX 1 AA1 ILE A 7 SER A 23 1 17 HELIX 2 AA2 THR A 28 ASN A 37 1 10 HELIX 3 AA3 SER A 39 LYS A 53 1 15 HELIX 4 AA4 ASP A 87 ASP A 97 1 11 HELIX 5 AA5 SER A 123 GLU A 136 1 14 HELIX 6 AA6 SER A 158 LYS A 172 1 15 SHEET 1 AA1 2 ILE A 57 THR A 60 0 SHEET 2 AA1 2 GLY A 63 TYR A 66 -1 O ILE A 65 N LEU A 58 SHEET 1 AA2 4 ALA A 75 GLN A 82 0 SHEET 2 AA2 4 VAL A 149 ALA A 156 -1 O HIS A 150 N CYS A 81 SHEET 3 AA2 4 LEU A 101 HIS A 109 -1 N LEU A 101 O GLU A 155 SHEET 4 AA2 4 GLY A 113 ALA A 117 -1 O ILE A 115 N VAL A 107 LINK OE1 GLU A 91 ZN ZN A 201 1555 1555 2.03 LINK OE2 GLU A 91 ZN ZN A 201 1555 1555 2.52 LINK NE2 HIS A 150 ZN ZN A 201 1555 1555 2.16 LINK NE2 HIS A 152 ZN ZN A 201 1555 1555 2.04 LINK ZN ZN A 201 O HOH A 398 1555 1555 2.35 CRYST1 42.365 42.365 176.203 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.023604 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005675 0.00000