HEADER TRANSFERASE 07-DEC-09 3KYZ TITLE THE CRYSTAL STRUCTURE OF THE SENSOR DOMAIN OF TWO-COMPONENT TITLE 2 SENSOR PFES FROM PSEUDOMONAS AERUGINOSA PA01 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN PFES; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 28-149; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: PA01; SOURCE 5 GENE: PFES, PA2687; 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: PMCSG19 KEYWDS APC37897.4, THE SENSOR DOMAIN OF TWO-COMPONENT SENSOR PFES, KEYWDS 2 PSEUDOMONAS AERUGINOSA PA01, STRUCTURAL GENOMICS, PSI-2, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 4 GENOMICS, MCSG, ATP-BINDING, CELL INNER MEMBRANE, CELL KEYWDS 5 MEMBRANE, KINASE, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 6 PHOSPHOPROTEIN, TRANSFERASE, TRANSMEMBRANE, TWO-COMPONENT KEYWDS 7 REGULATORY SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,N.MARSHALL,K.BUCK,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 1 19-JAN-10 3KYZ 0 JRNL AUTH K.TAN,N.MARSHALL,K.BUCK,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF THE SENSOR DOMAIN OF JRNL TITL 2 TWO-COMPONENT SENSOR PFES FROM PSEUDOMONAS JRNL TITL 3 AERUGINOSA PA01 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 23518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1198 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 35.1068 - 3.1135 0.99 2729 144 0.1697 0.1881 REMARK 3 2 3.1135 - 2.4715 1.00 2622 130 0.1571 0.1690 REMARK 3 3 2.4715 - 2.1591 1.00 2579 142 0.1334 0.1870 REMARK 3 4 2.1591 - 1.9617 0.99 2551 132 0.1135 0.1532 REMARK 3 5 1.9617 - 1.8211 0.99 2537 142 0.1068 0.1554 REMARK 3 6 1.8211 - 1.7137 0.97 2437 145 0.1051 0.1688 REMARK 3 7 1.7137 - 1.6279 0.95 2408 136 0.1109 0.1446 REMARK 3 8 1.6279 - 1.5571 0.91 2305 114 0.1328 0.1754 REMARK 3 9 1.5571 - 1.4971 0.85 2152 113 0.1693 0.2129 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 : 0.35 REMARK 3 B_SOL : 37.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.89120 REMARK 3 B22 (A**2) : -0.91660 REMARK 3 B33 (A**2) : 3.80780 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 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 : 0.005 999 REMARK 3 ANGLE : 0.957 1361 REMARK 3 CHIRALITY : 0.064 137 REMARK 3 PLANARITY : 0.004 182 REMARK 3 DIHEDRAL : 17.028 392 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 3KYZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB056623. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97932 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24347 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.73100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD/MLPHARE/DM/ARP/WARP/HKL3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGCL2, 0.1M BIS-TRIS, 25% REMARK 280 PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-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 14.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.78250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.73400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.78250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.73400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 14.96000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.73400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.78250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.73400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 14.96000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.78250 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: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 47.73400 REMARK 350 BIOMT3 2 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 25 REMARK 465 ASN A 26 REMARK 465 ALA A 27 REMARK 465 TRP A 28 REMARK 465 GLY A 29 REMARK 465 LEU A 30 REMARK 465 SER A 31 REMARK 465 VAL A 32 REMARK 465 GLU A 33 REMARK 465 ARG A 34 REMARK 465 SER A 35 REMARK 465 THR A 36 REMARK 465 GLY A 149 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 A 117 -76.54 -35.90 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 CL A 1 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 3 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 150 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC37897.4 RELATED DB: TARGETDB DBREF 3KYZ A 28 149 UNP Q04804 PFES_PSEAE 28 149 SEQADV 3KYZ SER A 25 UNP Q04804 EXPRESSION TAG SEQADV 3KYZ ASN A 26 UNP Q04804 EXPRESSION TAG SEQADV 3KYZ ALA A 27 UNP Q04804 EXPRESSION TAG SEQRES 1 A 125 SER ASN ALA TRP GLY LEU SER VAL GLU ARG SER THR TYR SEQRES 2 A 125 PHE LEU ALA PRO ALA ASP ARG HIS TYR LEU ALA ASP TYR SEQRES 3 A 125 ALA ARG GLN ALA GLU ASP ALA TRP ARG ARG GLU GLY ALA SEQRES 4 A 125 ALA GLY ALA GLU ARG PHE ARG LYS GLU LEU SER ALA LYS SEQRES 5 A 125 GLU ASP THR TRP VAL ALA LEU VAL GLY PRO HIS LEU GLU SEQRES 6 A 125 SER LEU GLY SER THR PRO LEU SER ALA GLU GLU SER SER SEQRES 7 A 125 HIS LEU THR PHE MSE ARG LYS LEU ASP TRP PRO MSE SER SEQRES 8 A 125 ARG ARG LEU GLN ASP GLU LEU PRO TYR VAL SER ILE GLU SEQRES 9 A 125 PHE PRO GLY HIS PRO GLU GLN GLY ARG LEU VAL ILE GLN SEQRES 10 A 125 LEU PRO GLU ARG LEU LEU PRO GLY MODRES 3KYZ MSE A 107 MET SELENOMETHIONINE MODRES 3KYZ MSE A 114 MET SELENOMETHIONINE HET MSE A 107 8 HET MSE A 114 8 HET CL A 1 1 HET CL A 2 1 HET CL A 3 1 HET FMT A 150 3 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM FMT FORMIC ACID FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 CL 3(CL 1-) FORMUL 5 FMT C H2 O2 FORMUL 6 HOH *149(H2 O) HELIX 1 1 ALA A 40 ASP A 78 1 39 HELIX 2 2 SER A 97 SER A 102 1 6 HELIX 3 3 HIS A 103 THR A 105 5 3 HELIX 4 4 HIS A 132 GLN A 135 5 4 HELIX 5 5 PRO A 143 LEU A 147 5 5 SHEET 1 A 3 VAL A 81 VAL A 84 0 SHEET 2 A 3 ARG A 137 GLN A 141 -1 O VAL A 139 N ALA A 82 SHEET 3 A 3 TYR A 124 GLU A 128 -1 N ILE A 127 O LEU A 138 LINK C PHE A 106 N MSE A 107 1555 1555 1.33 LINK C MSE A 107 N ARG A 108 1555 1555 1.33 LINK C PRO A 113 N MSE A 114 1555 1555 1.33 LINK C MSE A 114 N SER A 115 1555 1555 1.33 SITE 1 AC1 2 GLU A 128 HOH A 261 SITE 1 AC2 4 GLY A 85 PRO A 86 HIS A 87 GLU A 89 SITE 1 AC3 6 GLU A 89 SER A 90 PRO A 95 LEU A 96 SITE 2 AC3 6 HOH A 173 HOH A 242 SITE 1 AC4 2 GLN A 53 HOH A 163 CRYST1 29.920 95.468 103.565 90.00 90.00 90.00 I 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 0.033422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009656 0.00000