HEADER TRANSCRIPTION 26-AUG-19 6KTA TITLE CRYSTAL STRUCTURE OF B. HALODURANS MNTR IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HTH-TYPE TRANSCRIPTIONAL REGULATOR MNTR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MANGANESE TRANSPORT REGULATOR; COMPND 5 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: MNTR, BH2807; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MNTR, TRANSCRIPTION FACTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.LEE,M.Y.LEE REVDAT 2 27-MAR-24 6KTA 1 REMARK REVDAT 1 04-DEC-19 6KTA 0 JRNL AUTH M.Y.LEE,D.W.LEE,H.K.JOO,K.H.JEONG,J.Y.LEE JRNL TITL STRUCTURAL ANALYSIS OF THE MANGANESE TRANSPORT REGULATOR JRNL TITL 2 MNTR FROM BACILLUS HALODURANS IN APO AND MANGANESE BOUND JRNL TITL 3 FORMS. JRNL REF PLOS ONE V. 14 24689 2019 JRNL REFN ESSN 1932-6203 JRNL PMID 31738781 JRNL DOI 10.1371/JOURNAL.PONE.0224689 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 17896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 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 : 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 6KTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013606. 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 : 17942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM/POTASSIUM PHOSPHATE, MAGNESIUM REMARK 280 FORMATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 19.82950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.87850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.60150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.87850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.82950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.60150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU A 139 REMARK 465 GLU B 138 REMARK 465 GLU B 139 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 B 136 CG CD CE NZ 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 NE2 GLN A 44 O HOH A 401 2.06 REMARK 500 OH TYR A 75 O HOH A 402 2.12 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 B 58 -54.07 -130.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 202 DBREF 6KTA A 1 139 UNP Q9K943 MNTR_BACHD 1 139 DBREF 6KTA B 1 139 UNP Q9K943 MNTR_BACHD 1 139 SEQRES 1 A 139 MET PRO THR PRO SER MET GLU ASP TYR LEU GLU ARG ILE SEQRES 2 A 139 TYR LEU LEU ILE GLU GLU LYS GLY TYR ALA ARG VAL SER SEQRES 3 A 139 ASP ILE ALA GLU ALA LEU GLU VAL HIS PRO SER SER VAL SEQRES 4 A 139 THR LYS MET VAL GLN LYS LEU ASP LYS SER ASP TYR LEU SEQRES 5 A 139 VAL TYR GLU ARG TYR ARG GLY LEU ILE LEU THR ALA LYS SEQRES 6 A 139 GLY LYS LYS ILE GLY LYS ARG LEU VAL TYR ARG HIS ASP SEQRES 7 A 139 LEU LEU GLU ASP PHE LEU LYS MET ILE GLY VAL ASP SER SEQRES 8 A 139 ASP HIS ILE TYR GLU ASP VAL GLU GLY ILE GLU HIS HIS SEQRES 9 A 139 LEU SER TRP ASP ALA ILE ASP ARG ILE GLY ASP LEU VAL SEQRES 10 A 139 GLN TYR PHE GLN GLU ASP PRO SER ARG LEU ASN ASP LEU SEQRES 11 A 139 ARG GLU VAL GLN LYS LYS ASN GLU GLU SEQRES 1 B 139 MET PRO THR PRO SER MET GLU ASP TYR LEU GLU ARG ILE SEQRES 2 B 139 TYR LEU LEU ILE GLU GLU LYS GLY TYR ALA ARG VAL SER SEQRES 3 B 139 ASP ILE ALA GLU ALA LEU GLU VAL HIS PRO SER SER VAL SEQRES 4 B 139 THR LYS MET VAL GLN LYS LEU ASP LYS SER ASP TYR LEU SEQRES 5 B 139 VAL TYR GLU ARG TYR ARG GLY LEU ILE LEU THR ALA LYS SEQRES 6 B 139 GLY LYS LYS ILE GLY LYS ARG LEU VAL TYR ARG HIS ASP SEQRES 7 B 139 LEU LEU GLU ASP PHE LEU LYS MET ILE GLY VAL ASP SER SEQRES 8 B 139 ASP HIS ILE TYR GLU ASP VAL GLU GLY ILE GLU HIS HIS SEQRES 9 B 139 LEU SER TRP ASP ALA ILE ASP ARG ILE GLY ASP LEU VAL SEQRES 10 B 139 GLN TYR PHE GLN GLU ASP PRO SER ARG LEU ASN ASP LEU SEQRES 11 B 139 ARG GLU VAL GLN LYS LYS ASN GLU GLU HET GOL A 301 6 HET GOL A 302 6 HET GOL B 201 6 HET GOL B 202 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 HOH *135(H2 O) HELIX 1 AA1 THR A 3 GLY A 21 1 19 HELIX 2 AA2 ARG A 24 GLU A 33 1 10 HELIX 3 AA3 HIS A 35 SER A 49 1 15 HELIX 4 AA4 THR A 63 GLY A 88 1 26 HELIX 5 AA5 HIS A 93 HIS A 103 1 11 HELIX 6 AA6 SER A 106 ASP A 123 1 18 HELIX 7 AA7 PRO A 124 GLU A 138 1 15 HELIX 8 AA8 THR B 3 GLY B 21 1 19 HELIX 9 AA9 ARG B 24 GLU B 33 1 10 HELIX 10 AB1 HIS B 35 SER B 49 1 15 HELIX 11 AB2 THR B 63 ILE B 87 1 25 HELIX 12 AB3 HIS B 93 HIS B 103 1 11 HELIX 13 AB4 SER B 106 ASP B 123 1 18 HELIX 14 AB5 PRO B 124 ASN B 137 1 14 SHEET 1 AA1 2 LEU A 52 GLU A 55 0 SHEET 2 AA1 2 GLY A 59 LEU A 62 -1 O ILE A 61 N VAL A 53 SHEET 1 AA2 2 LEU B 52 GLU B 55 0 SHEET 2 AA2 2 GLY B 59 LEU B 62 -1 O GLY B 59 N GLU B 55 SITE 1 AC1 6 ASP A 47 VAL A 53 TYR A 54 LEU B 62 SITE 2 AC1 6 ALA B 64 LYS B 67 SITE 1 AC2 4 GLU A 55 HIS A 77 GLU A 81 TYR B 22 SITE 1 AC3 8 THR A 63 ALA A 64 LYS A 67 ASP B 47 SITE 2 AC3 8 VAL B 53 TYR B 54 HOH B 344 HOH B 358 SITE 1 AC4 1 HOH B 322 CRYST1 39.659 89.203 109.757 90.00 90.00 90.00 P 21 21 21 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 0.025215 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009111 0.00000