HEADER SIGNALING PROTEIN, CELL CYCLE 10-JUL-02 1M5U TITLE CRYSTAL STRUCTURE OF THE RESPONSE REGULATOR DIVK. STRUCTURE AT PH 8.0 TITLE 2 IN THE APO-FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION RESPONSE REGULATOR DIVK; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POLAR DIFFERENTIATION RESPONSE REGULATOR; CHEY HOMOLOG DIVK; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: STRUCTURE AT PH 8.0 IN THE APO-FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES; SOURCE 3 ORGANISM_TAXID: 155892; SOURCE 4 GENE: DIVK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-DE3-PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT7-7 PZHF55 KEYWDS RESPONSE REGULATOR, SIGNAL TRANSDUCTION PROTEIN, STRUCTURAL KEYWDS 2 PROTEOMICS IN EUROPE, SPINE, STRUCTURAL GENOMICS, SIGNALING PROTEIN, KEYWDS 3 CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR V.GUILLET,N.OHTA,S.CABANTOUS,A.NEWTON,J.-P.SAMAMA,STRUCTURAL AUTHOR 2 PROTEOMICS IN EUROPE (SPINE) REVDAT 4 03-APR-24 1M5U 1 REMARK REVDAT 3 14-FEB-24 1M5U 1 REMARK REVDAT 2 24-FEB-09 1M5U 1 VERSN REVDAT 1 15-NOV-02 1M5U 0 JRNL AUTH V.GUILLET,N.OHTA,S.CABANTOUS,A.NEWTON,J.-P.SAMAMA JRNL TITL CRYSTALLOGRAPHIC AND BIOCHEMICAL STUDIES OF DIVK REVEAL JRNL TITL 2 NOVEL FEATURES OF AN ESSENTIAL RESPONSE REGULATOR IN JRNL TITL 3 CAULOBACTER CRESCENTUS JRNL REF J.BIOL.CHEM. V. 277 42003 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12176983 JRNL DOI 10.1074/JBC.M204789200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.CABANTOUS,V.GUILLET,N.OHTA,A.NEWTON,J.-P.SAMAMA REMARK 1 TITL CHARACTERIZATION AND CRYSTALLIZATION OF DIVK, AN ESSENTIAL REMARK 1 TITL 2 RESPONSE REGULATOR FOR CELL DIVISION AND DIFFERENTIATION IN REMARK 1 TITL 3 CAULOBACTER CRESCENTUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1249 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444902008338 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.B.HECHT,T.LANE,N.OHTA,J.M.SOMMER,A.NEWTON REMARK 1 TITL AN ESSENTIAL SINGLE DOMAIN RESPONSE REGULATOR REQUIRED FOR REMARK 1 TITL 2 NORMAL CELL DIVISION AND DIFFERENTIATION IN CAULOBACTER REMARK 1 TITL 3 CRESCENTUS REMARK 1 REF EMBO J. V. 14 3915 1995 REMARK 1 REFN ISSN 0261-4189 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 8022 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 854 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1044 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 127 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 872 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 1.45000 REMARK 3 B33 (A**2) : -1.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.160 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.780 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.640 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.410 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.52 REMARK 3 BSOL : 111.6 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016635. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : SI111 OR SI311 CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.09700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: APO-DIVK SOLVED AT PH6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES 50MM PH6.0,PEG MME 550 32% AT REMARK 280 285K. THE PROTEIN WAS CONCENTRATED AT 2 MG/ML IN MES-NAOH PH REMARK 280 6.00 (20 MM), DTT (5 MM) AND MIXED WITH AN EQUAL VOLUME OF THE REMARK 280 RESERVOIR SOLUTION CONTAINING PEG MME 550 (32%), MES PH 6.00 (40 REMARK 280 MM), DTT (5MM). CRYSTAL SIZE (300X40X40 MICROM3) IN 20MICROL REMARK 280 SITTING DROPS. VAPOR DIFFUSION, HANGING OR SITTING-DROP AT 285K. REMARK 280 CRYSTALS WERE TRANSFERRED IN RESERVOIR SOLUTIONS WHOSE PH WAS REMARK 280 INCREASED FROM 6.0 TO 8.0 BY STEPS OF 0.5 PH UNITS (THE SOAKING REMARK 280 TIME IN EACH SOLUTION WAS 12 HOURS). CRYSTALS WERE FROZEN IN REMARK 280 LIQUID PROPANE AFTER SOAKING FOR A FEW SECONDS IN PEG MME 550 REMARK 280 (50%), TRIS PH 8.0 (40 MM)., PH 8.00 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 18.33500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.14500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.35500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.14500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.33500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.35500 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: MONOMERIC 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 PHE A 85 REMARK 465 ALA A 86 REMARK 465 MET A 87 REMARK 465 LYS A 88 REMARK 465 GLY A 89 REMARK 465 ASP A 90 REMARK 465 GLU A 91 REMARK 465 GLU A 92 REMARK 465 ARG A 93 REMARK 465 GLU A 96 REMARK 465 ALA A 125 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 A 46 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ARG A 95 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 102 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 105 CG CD CE NZ 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 70.31 43.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M5T RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 6.0 REMARK 900 RELATED ID: IGBMC-1121-000 RELATED DB: TARGETDB DBREF 1M5U A 2 125 UNP Q9A5I4 Q9A5I4_CAUCR 2 125 SEQRES 1 A 124 THR LYS LYS VAL LEU ILE VAL GLU ASP ASN GLU LEU ASN SEQRES 2 A 124 MET LYS LEU PHE HIS ASP LEU LEU GLU ALA GLN GLY TYR SEQRES 3 A 124 GLU THR LEU GLN THR ARG GLU GLY LEU SER ALA LEU SER SEQRES 4 A 124 ILE ALA ARG GLU ASN LYS PRO ASP LEU ILE LEU MET ASP SEQRES 5 A 124 ILE GLN LEU PRO GLU ILE SER GLY LEU GLU VAL THR LYS SEQRES 6 A 124 TRP LEU LYS GLU ASP ASP ASP LEU ALA HIS ILE PRO VAL SEQRES 7 A 124 VAL ALA VAL THR ALA PHE ALA MET LYS GLY ASP GLU GLU SEQRES 8 A 124 ARG ILE ARG GLU GLY GLY CYS GLU ALA TYR ILE SER LYS SEQRES 9 A 124 PRO ILE SER VAL VAL HIS PHE LEU GLU THR ILE LYS ARG SEQRES 10 A 124 LEU LEU GLU ARG GLN PRO ALA FORMUL 2 HOH *64(H2 O) HELIX 1 1 ASN A 11 ALA A 24 1 14 HELIX 2 2 GLU A 34 LYS A 46 1 13 HELIX 3 3 SER A 60 ASP A 71 1 12 HELIX 4 4 SER A 108 GLU A 121 1 14 SHEET 1 A 5 GLU A 28 THR A 32 0 SHEET 2 A 5 LYS A 4 VAL A 8 1 N ILE A 7 O LEU A 30 SHEET 3 A 5 LEU A 49 ASP A 53 1 O LEU A 51 N VAL A 8 SHEET 4 A 5 VAL A 79 THR A 83 1 O VAL A 80 N ILE A 50 SHEET 5 A 5 ALA A 101 SER A 104 1 O ALA A 101 N ALA A 81 CISPEP 1 LYS A 105 PRO A 106 0 -0.12 CRYST1 36.670 40.710 66.290 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 0.027270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015085 0.00000