HEADER TRANSCRIPTION REGULATOR 20-APR-10 3MN2 TITLE THE CRYSTAL STRUCTURE OF A PROBABLE ARAC FAMILY TRANSCRIPTIONAL TITLE 2 REGULATOR FROM RHODOPSEUDOMONAS PALUSTRIS CGA009 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ARAC FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 258594; SOURCE 4 STRAIN: CGA009; SOURCE 5 GENE: RPA0567; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PPK1037; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19B KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, MCSG, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,H.LI,K.BUCK,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 2 27-NOV-24 3MN2 1 REMARK LINK REVDAT 1 12-MAY-10 3MN2 0 JRNL AUTH K.TAN,H.LI,K.BUCK,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF A PROBABLE ARAC FAMILY JRNL TITL 2 TRANSCRIPTIONAL REGULATOR FROM RHODOPSEUDOMONAS PALUSTRIS JRNL TITL 3 CGA009 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 18473 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 943 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 20.9821 - 3.4379 0.96 2555 108 0.1893 0.2165 REMARK 3 2 3.4379 - 2.7307 1.00 2576 141 0.1966 0.2381 REMARK 3 3 2.7307 - 2.3861 0.99 2566 132 0.1956 0.2785 REMARK 3 4 2.3861 - 2.1682 0.99 2549 145 0.1974 0.2573 REMARK 3 5 2.1682 - 2.0129 0.98 2503 153 0.2027 0.2755 REMARK 3 6 2.0129 - 1.8943 0.96 2461 135 0.2272 0.2571 REMARK 3 7 1.8943 - 1.7995 0.90 2320 129 0.2395 0.2752 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 : 0.38 REMARK 3 B_SOL : 57.52 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 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 : 0.007 1760 REMARK 3 ANGLE : 1.000 2377 REMARK 3 CHIRALITY : 0.064 254 REMARK 3 PLANARITY : 0.004 311 REMARK 3 DIHEDRAL : 16.127 655 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 6.4780 44.6813 20.6078 REMARK 3 T TENSOR REMARK 3 T11: 0.1747 T22: 0.1419 REMARK 3 T33: 0.2182 T12: -0.0063 REMARK 3 T13: 0.0356 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.5102 L22: 1.5361 REMARK 3 L33: 1.5572 L12: -0.9162 REMARK 3 L13: -0.8746 L23: 1.4317 REMARK 3 S TENSOR REMARK 3 S11: 0.0801 S12: -0.1112 S13: 0.2927 REMARK 3 S21: 0.0239 S22: 0.1408 S23: -0.2120 REMARK 3 S31: 0.0333 S32: 0.0676 S33: -0.2174 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 3MN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18976 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 21.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.71400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, MLPHARE, HKL-3000, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPHATE-CITRATE 40% V/V PEG300, REMARK 280 PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.72533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.36267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.04400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.68133 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.40667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: EXPERIMENTALLY UNKNOWN. THE MOLECULE IS LIKELY MONOMERIC. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 THR A 285 77.30 -159.50 REMARK 500 ALA B 284 -51.45 -135.23 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 PO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC66556.1 RELATED DB: TARGETDB DBREF 3MN2 A 221 325 UNP Q6NCA5 Q6NCA5_RHOPA 221 325 DBREF 3MN2 B 221 325 UNP Q6NCA5 Q6NCA5_RHOPA 221 325 SEQADV 3MN2 SER A 218 UNP Q6NCA5 EXPRESSION TAG SEQADV 3MN2 ASN A 219 UNP Q6NCA5 EXPRESSION TAG SEQADV 3MN2 ALA A 220 UNP Q6NCA5 EXPRESSION TAG SEQADV 3MN2 SER B 218 UNP Q6NCA5 EXPRESSION TAG SEQADV 3MN2 ASN B 219 UNP Q6NCA5 EXPRESSION TAG SEQADV 3MN2 ALA B 220 UNP Q6NCA5 EXPRESSION TAG SEQRES 1 A 108 SER ASN ALA VAL ARG GLN VAL GLU GLU TYR ILE GLU ALA SEQRES 2 A 108 ASN TRP MSE ARG PRO ILE THR ILE GLU LYS LEU THR ALA SEQRES 3 A 108 LEU THR GLY ILE SER SER ARG GLY ILE PHE LYS ALA PHE SEQRES 4 A 108 GLN ARG SER ARG GLY TYR SER PRO MSE ALA PHE ALA LYS SEQRES 5 A 108 ARG VAL ARG LEU GLN HIS ALA HIS ASN LEU LEU SER ASP SEQRES 6 A 108 GLY ALA THR PRO THR THR VAL THR ALA ALA ALA LEU SER SEQRES 7 A 108 CYS GLY PHE SER ASN LEU GLY HIS PHE ALA ARG ASP TYR SEQRES 8 A 108 ARG ASP MSE PHE GLY GLU LYS PRO SER GLU THR LEU GLN SEQRES 9 A 108 ARG ALA ARG PRO SEQRES 1 B 108 SER ASN ALA VAL ARG GLN VAL GLU GLU TYR ILE GLU ALA SEQRES 2 B 108 ASN TRP MSE ARG PRO ILE THR ILE GLU LYS LEU THR ALA SEQRES 3 B 108 LEU THR GLY ILE SER SER ARG GLY ILE PHE LYS ALA PHE SEQRES 4 B 108 GLN ARG SER ARG GLY TYR SER PRO MSE ALA PHE ALA LYS SEQRES 5 B 108 ARG VAL ARG LEU GLN HIS ALA HIS ASN LEU LEU SER ASP SEQRES 6 B 108 GLY ALA THR PRO THR THR VAL THR ALA ALA ALA LEU SER SEQRES 7 B 108 CYS GLY PHE SER ASN LEU GLY HIS PHE ALA ARG ASP TYR SEQRES 8 B 108 ARG ASP MSE PHE GLY GLU LYS PRO SER GLU THR LEU GLN SEQRES 9 B 108 ARG ALA ARG PRO MODRES 3MN2 MSE A 233 MET SELENOMETHIONINE MODRES 3MN2 MSE A 265 MET SELENOMETHIONINE MODRES 3MN2 MSE A 311 MET SELENOMETHIONINE MODRES 3MN2 MSE B 233 MET SELENOMETHIONINE MODRES 3MN2 MSE B 265 MET SELENOMETHIONINE MODRES 3MN2 MSE B 311 MET SELENOMETHIONINE HET MSE A 233 8 HET MSE A 265 8 HET MSE A 311 8 HET MSE B 233 8 HET MSE B 265 8 HET MSE B 311 8 HET PO4 A 1 5 HET PO4 A 2 5 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *141(H2 O) HELIX 1 1 SER A 218 TRP A 232 1 15 HELIX 2 2 THR A 237 GLY A 246 1 10 HELIX 3 3 SER A 248 ARG A 260 1 13 HELIX 4 4 SER A 263 ASP A 282 1 20 HELIX 5 5 THR A 288 CYS A 296 1 9 HELIX 6 6 ASN A 300 GLY A 313 1 14 HELIX 7 7 LYS A 315 ALA A 323 1 9 HELIX 8 8 SER B 218 TRP B 232 1 15 HELIX 9 9 THR B 237 GLY B 246 1 10 HELIX 10 10 SER B 248 ARG B 260 1 13 HELIX 11 11 SER B 263 ASP B 282 1 20 HELIX 12 12 THR B 288 CYS B 296 1 9 HELIX 13 13 ASN B 300 GLY B 313 1 14 HELIX 14 14 LYS B 315 ALA B 323 1 9 LINK C TRP A 232 N MSE A 233 1555 1555 1.34 LINK C MSE A 233 N ARG A 234 1555 1555 1.33 LINK C PRO A 264 N MSE A 265 1555 1555 1.34 LINK C MSE A 265 N ALA A 266 1555 1555 1.33 LINK C ASP A 310 N MSE A 311 1555 1555 1.33 LINK C MSE A 311 N PHE A 312 1555 1555 1.33 LINK C TRP B 232 N MSE B 233 1555 1555 1.33 LINK C MSE B 233 N ARG B 234 1555 1555 1.33 LINK C PRO B 264 N MSE B 265 1555 1555 1.34 LINK C MSE B 265 N ALA B 266 1555 1555 1.33 LINK C ASP B 310 N MSE B 311 1555 1555 1.33 LINK C MSE B 311 N PHE B 312 1555 1555 1.33 SITE 1 AC1 5 HOH A 123 PHE A 298 SER A 299 ASN A 300 SITE 2 AC1 5 GLN B 257 SITE 1 AC2 8 HOH A 124 ILE A 236 THR A 237 ILE A 238 SITE 2 AC2 8 LEU A 241 PRO A 264 MSE A 265 ALA A 268 CRYST1 64.097 64.097 88.088 90.00 90.00 120.00 P 65 12 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 0.015601 0.009007 0.000000 0.00000 SCALE2 0.000000 0.018015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011352 0.00000