HEADER SIGNALING PROTEIN 18-MAY-15 4ZVD TITLE CRYSTAL STRUCTURE OF MID DOMAIN OF THE E. COLI DOSC - FORM II COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIGUANYLATE CYCLASE DOSC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 173-298; COMPND 5 SYNONYM: DGC,DIRECT OXYGEN-SENSING CYCLASE; COMPND 6 EC: 2.7.7.65; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DOSC, YDDV, B1490, JW5241; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYGEN SENSING, DIGUANYLATE CYCLASE, CYCLIC-DI-GMP, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.TARNAWSKI,T.R.M.BARENDS,I.SCHLICHTING REVDAT 2 10-JAN-24 4ZVD 1 REMARK REVDAT 1 11-NOV-15 4ZVD 0 JRNL AUTH M.TARNAWSKI,T.R.BARENDS,I.SCHLICHTING JRNL TITL STRUCTURAL ANALYSIS OF AN OXYGEN-REGULATED DIGUANYLATE JRNL TITL 2 CYCLASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 2158 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26527135 JRNL DOI 10.1107/S139900471501545X REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 817 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 46.3388 - 3.4523 1.00 2721 144 0.2264 0.2538 REMARK 3 2 3.4523 - 2.7403 1.00 2606 137 0.2500 0.3027 REMARK 3 3 2.7403 - 2.3939 1.00 2584 136 0.2388 0.2656 REMARK 3 4 2.3939 - 2.1750 1.00 2548 134 0.2306 0.3077 REMARK 3 5 2.1750 - 2.0191 1.00 2541 134 0.2369 0.3224 REMARK 3 6 2.0191 - 1.9001 1.00 2509 132 0.2736 0.3703 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.160 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 : 0.004 1900 REMARK 3 ANGLE : 0.723 2561 REMARK 3 CHIRALITY : 0.029 287 REMARK 3 PLANARITY : 0.003 329 REMARK 3 DIHEDRAL : 12.069 711 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 4ZVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99999 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 : 12.50 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 0.62400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.480 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: 4ZVC 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: 0.2M AMMONIUM DIHYDROGEN PHOSPHATE, REMARK 280 20% (W/V) PEG 3350, VAPOR DIFFUSION, TEMPERATURE 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 20.96500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.32500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.63000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.32500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.96500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.63000 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: 2020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 SER A 173 REMARK 465 LEU A 174 REMARK 465 LEU A 175 REMARK 465 GLU A 176 REMARK 465 ASN A 177 REMARK 465 SER A 291 REMARK 465 ARG A 292 REMARK 465 HIS A 293 REMARK 465 GLU A 294 REMARK 465 VAL A 295 REMARK 465 GLY A 296 REMARK 465 MET A 297 REMARK 465 ASP A 298 REMARK 465 SER B 173 REMARK 465 LEU B 174 REMARK 465 LEU B 175 REMARK 465 GLU B 176 REMARK 465 ASN B 177 REMARK 465 SER B 291 REMARK 465 ARG B 292 REMARK 465 HIS B 293 REMARK 465 GLU B 294 REMARK 465 VAL B 295 REMARK 465 GLY B 296 REMARK 465 MET B 297 REMARK 465 ASP B 298 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 HOH A 310 O HOH A 320 2.18 REMARK 500 OE1 GLN A 271 O HOH A 301 2.19 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 ASN A 255 71.86 -164.82 REMARK 500 ASN B 255 68.63 -161.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 4ZVD A 173 298 UNP P0AA89 DOSC_ECOLI 173 298 DBREF 4ZVD B 173 298 UNP P0AA89 DOSC_ECOLI 173 298 SEQRES 1 A 126 SER LEU LEU GLU ASN ALA GLU GLU GLU LYS GLU ARG GLN SEQRES 2 A 126 ILE ALA SER ILE LEU SER TRP GLU ILE ASP ILE ILE TYR SEQRES 3 A 126 LYS ILE LEU LEU ASP SER ASP LEU GLY SER SER LEU PRO SEQRES 4 A 126 LEU SER GLN ALA ASP PHE GLY LEU TRP PHE ASN HIS LYS SEQRES 5 A 126 GLY ARG HIS TYR PHE SER GLY ILE ALA GLU VAL GLY HIS SEQRES 6 A 126 ILE SER ARG LEU ILE GLN ASP PHE ASP GLY ILE PHE ASN SEQRES 7 A 126 GLN THR MET ARG ASN THR ARG ASN LEU ASN ASN ARG SER SEQRES 8 A 126 LEU ARG VAL LYS PHE LEU LEU GLN ILE ARG ASN THR VAL SEQRES 9 A 126 SER GLN ILE ILE THR LEU LEU ARG GLU LEU PHE GLU GLU SEQRES 10 A 126 VAL SER ARG HIS GLU VAL GLY MET ASP SEQRES 1 B 126 SER LEU LEU GLU ASN ALA GLU GLU GLU LYS GLU ARG GLN SEQRES 2 B 126 ILE ALA SER ILE LEU SER TRP GLU ILE ASP ILE ILE TYR SEQRES 3 B 126 LYS ILE LEU LEU ASP SER ASP LEU GLY SER SER LEU PRO SEQRES 4 B 126 LEU SER GLN ALA ASP PHE GLY LEU TRP PHE ASN HIS LYS SEQRES 5 B 126 GLY ARG HIS TYR PHE SER GLY ILE ALA GLU VAL GLY HIS SEQRES 6 B 126 ILE SER ARG LEU ILE GLN ASP PHE ASP GLY ILE PHE ASN SEQRES 7 B 126 GLN THR MET ARG ASN THR ARG ASN LEU ASN ASN ARG SER SEQRES 8 B 126 LEU ARG VAL LYS PHE LEU LEU GLN ILE ARG ASN THR VAL SEQRES 9 B 126 SER GLN ILE ILE THR LEU LEU ARG GLU LEU PHE GLU GLU SEQRES 10 B 126 VAL SER ARG HIS GLU VAL GLY MET ASP FORMUL 3 HOH *62(H2 O) HELIX 1 AA1 ALA A 178 SER A 204 1 27 HELIX 2 AA2 PRO A 211 GLN A 214 5 4 HELIX 3 AA3 ALA A 215 LYS A 224 1 10 HELIX 4 AA4 LYS A 224 PHE A 229 1 6 HELIX 5 AA5 ALA A 233 ARG A 254 1 22 HELIX 6 AA6 ASN A 261 VAL A 290 1 30 HELIX 7 AA7 GLU B 179 SER B 204 1 26 HELIX 8 AA8 PRO B 211 GLN B 214 5 4 HELIX 9 AA9 ALA B 215 LYS B 224 1 10 HELIX 10 AB1 LYS B 224 PHE B 229 1 6 HELIX 11 AB2 ILE B 232 ARG B 254 1 23 HELIX 12 AB3 ARG B 257 ASN B 260 5 4 HELIX 13 AB4 ASN B 261 VAL B 290 1 30 CRYST1 41.930 51.260 92.650 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 0.023849 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010793 0.00000