HEADER DNA BINDING PROTEIN 20-SEP-18 6MJ1 TITLE CRYSTAL STRUCTURE OF REFZ (REGULATOR OF FTSZ) FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE HTH-TYPE TRANSCRIPTIONAL REGULATOR YTTP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STRESS RESPONSE PROTEIN YTTP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YTTP, BSU29630; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TETR FAMILY, CELL DIVISION, FTSZ REGULATOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.V.KRIEGER,E.E.BROWN,J.K.HERMAN,J.C.SACCHETTINI REVDAT 6 13-MAR-24 6MJ1 1 REMARK REVDAT 5 30-SEP-20 6MJ1 1 JRNL REVDAT 4 27-NOV-19 6MJ1 1 REMARK REVDAT 3 07-AUG-19 6MJ1 1 JRNL REVDAT 2 19-JUN-19 6MJ1 1 JRNL REVDAT 1 20-MAR-19 6MJ1 0 JRNL AUTH E.E.BROWN,A.K.MILLER,I.V.KRIEGER,R.M.OTTO,J.C.SACCHETTINI, JRNL AUTH 2 J.K.HERMAN JRNL TITL A DNA-BINDING PROTEIN TUNES SEPTUM PLACEMENT DURING BACILLUS JRNL TITL 2 SUBTILIS SPORULATION. JRNL REF J.BACTERIOL. V. 201 2019 JRNL REFN ESSN 1098-5530 JRNL PMID 31160399 JRNL DOI 10.1128/JB.00287-19 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 16039 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 : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.580 REMARK 3 FREE R VALUE TEST SET COUNT : 734 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 44.7513 - 4.4448 1.00 3225 184 0.1782 0.2086 REMARK 3 2 4.4448 - 3.5284 0.99 3077 126 0.2210 0.2429 REMARK 3 3 3.5284 - 3.0825 0.97 2964 152 0.2768 0.3308 REMARK 3 4 3.0825 - 2.8007 0.99 3026 132 0.3056 0.3955 REMARK 3 5 2.8007 - 2.6000 1.00 3013 140 0.3390 0.3632 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.810 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 : 0.009 1730 REMARK 3 ANGLE : 1.082 2335 REMARK 3 CHIRALITY : 0.056 257 REMARK 3 PLANARITY : 0.007 290 REMARK 3 DIHEDRAL : 7.426 1469 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 6MJ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000236976. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16237 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 : 17.59 REMARK 200 R MERGE (I) : 0.11270 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.05 REMARK 200 R MERGE FOR SHELL (I) : 0.79290 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% ETHANOL (V/V), 0.1 M IMIDAZOLE [PH REMARK 280 8.0], AND 0.2 M MGCL2, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 50.08850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.01050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.01050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.04425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.01050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.01050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.13275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.01050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.01050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.04425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.01050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.01050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.13275 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 50.08850 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: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 319 LIES ON A SPECIAL POSITION. 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 GLY A 201 REMARK 465 ASP A 202 REMARK 465 VAL A 203 REMARK 465 ALA A 204 REMARK 465 LEU A 205 REMARK 465 THR A 206 REMARK 465 ASN A 207 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 LYS A 46 -40.29 75.78 REMARK 500 ASN A 73 15.52 -172.16 REMARK 500 THR A 109 -101.13 -70.53 REMARK 500 ILE A 110 -168.55 54.10 REMARK 500 ASP A 111 111.27 69.16 REMARK 500 SER A 112 64.49 -169.00 REMARK 500 THR A 113 -70.87 42.53 REMARK 500 LYS A 139 46.62 -83.07 REMARK 500 GLN A 140 151.53 174.14 REMARK 500 ARG A 141 47.06 -82.41 REMARK 500 LEU A 164 -63.17 -128.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6MJ1 A 1 207 UNP O34970 YTTP_BACSU 1 207 SEQRES 1 A 207 MET LYS VAL SER THR LYS ASP LYS ILE ILE GLU SER ALA SEQRES 2 A 207 VAL MET LEU PHE ASN GLN LYS GLY PHE SER GLY THR SER SEQRES 3 A 207 VAL ARG GLU ILE ALA LYS SER ALA ASP VAL ASN VAL ALA SEQRES 4 A 207 HIS ILE SER TYR TYR PHE LYS GLY LYS GLY GLY LEU MET SEQRES 5 A 207 GLU HIS LEU VAL SER GLU PHE TYR GLU GLY TYR SER LYS SEQRES 6 A 207 THR LEU GLU THR ALA ALA SER ASN ILE SER THR GLN SER SEQRES 7 A 207 THR GLN GLU GLN LEU LEU GLN LEU VAL PHE ASP ILE LEU SEQRES 8 A 207 SER TYR GLN HIS ASN HIS ARG GLN LEU THR ARG PHE VAL SEQRES 9 A 207 TYR ARG GLU VAL THR ILE ASP SER THR LEU ILE ARG GLU SEQRES 10 A 207 ILE MET SER THR TYR LEU MET LYS GLU LYS TYR ILE PHE SEQRES 11 A 207 GLN LEU ILE ILE GLU GLU GLY GLU LYS GLN ARG GLU TYR SEQRES 12 A 207 LEU THR LEU PRO LEU PRO HIS PHE ILE LEU GLN LEU LYS SEQRES 13 A 207 SER LEU LEU MET MET PRO TYR LEU GLN PRO GLN TYR ILE SEQRES 14 A 207 SER GLU VAL LEU TYR MET GLN PRO HIS GLU PRO TYR PHE SEQRES 15 A 207 TYR LYS MET TYR PHE GLU GLU ILE LYS ILE TRP ILE ARG SEQRES 16 A 207 SER VAL PHE ARG THR GLY ASP VAL ALA LEU THR ASN FORMUL 2 HOH *25(H2 O) HELIX 1 AA1 SER A 4 LYS A 20 1 17 HELIX 2 AA2 SER A 26 ASP A 35 1 10 HELIX 3 AA3 ASN A 37 LYS A 46 1 10 HELIX 4 AA4 GLY A 47 SER A 72 1 26 HELIX 5 AA5 SER A 78 HIS A 97 1 20 HELIX 6 AA6 HIS A 97 GLU A 107 1 11 HELIX 7 AA7 THR A 113 GLU A 138 1 26 HELIX 8 AA8 PRO A 147 MET A 161 1 15 HELIX 9 AA9 PRO A 162 LEU A 164 5 3 HELIX 10 AB1 GLN A 165 MET A 175 1 11 HELIX 11 AB2 PHE A 182 VAL A 197 1 16 SHEET 1 AA1 2 TYR A 143 LEU A 144 0 SHEET 2 AA1 2 PHE A 198 ARG A 199 -1 O ARG A 199 N TYR A 143 CRYST1 100.021 100.021 100.177 90.00 90.00 90.00 P 41 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 0.009998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009998 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009982 0.00000