HEADER TRANSFERASE 05-NOV-09 3KKB TITLE THE CRYSTAL STRUCTURE OF A TWO-COMPONENT SENSOR DOMAIN FROM TITLE 2 PSEUDOMONAS AERUGINOSA PA01 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: A TWO-COMPONENT SENSOR DOMAIN; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PA01; SOURCE 5 GENE: PA5484, PSEUDOMONAS AERUGINOSA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG9 KEYWDS APC37838.3, TWO-COMPONENT SENSOR, PSEUDOMONAS AERUGINOSA KEYWDS 2 PA01, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, KEYWDS 4 ATP-BINDING, KINASE, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 5 PHOSPHOPROTEIN, TRANSFERASE, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,G.CHHOR,K.BUCK,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 1 17-NOV-09 3KKB 0 JRNL AUTH K.TAN,G.CHHOR,K.BUCK,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF A TWO-COMPONENT SENSOR JRNL TITL 2 DOMAIN FROM PSEUDOMONAS AERUGINOSA PA01 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.88 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 19520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 982 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 37.6880 - 3.5979 1.00 2890 156 0.1705 0.1998 REMARK 3 2 3.5979 - 2.8560 0.99 2793 121 0.1572 0.2468 REMARK 3 3 2.8560 - 2.4951 0.99 2718 149 0.1611 0.2260 REMARK 3 4 2.4951 - 2.2670 0.98 2669 157 0.1557 0.2184 REMARK 3 5 2.2670 - 2.1045 0.96 2655 140 0.1448 0.2118 REMARK 3 6 2.1045 - 1.9805 0.95 2573 142 0.1625 0.2146 REMARK 3 7 1.9805 - 1.8813 0.82 2240 117 0.1906 0.2472 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 : 0.34 REMARK 3 B_SOL : 35.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 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 : 0.006 2040 REMARK 3 ANGLE : 0.876 2766 REMARK 3 CHIRALITY : 0.056 309 REMARK 3 PLANARITY : 0.003 383 REMARK 3 DIHEDRAL : 18.157 776 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): -5.0030 38.2471 21.8802 REMARK 3 T TENSOR REMARK 3 T11: 0.1002 T22: 0.0835 REMARK 3 T33: 0.1240 T12: -0.0226 REMARK 3 T13: -0.0057 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.1855 L22: 0.7991 REMARK 3 L33: 0.7307 L12: -0.2714 REMARK 3 L13: -0.3663 L23: -0.3408 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: 0.0348 S13: -0.1617 REMARK 3 S21: 0.0203 S22: -0.0181 S23: -0.0124 REMARK 3 S31: 0.1450 S32: -0.0425 S33: 0.0218 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 3KKB COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-09. REMARK 100 THE RCSB ID CODE IS RCSB056098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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) : 0.97942 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 : 20202 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 41.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPHATE-CITRATE, 1.6M REMARK 280 NAH2PO4 /0.4M K2HPO4, PH 4.2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 50.01333 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 25.00667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.00667 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 50.01333 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 300 REMARK: EXPERIMENTALLY UNKNOWN. THE CHAINS A AND B ARE PREDICTED REMARK 300 TO FORM A DIMER. 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 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 ARG A 165 REMARK 465 HIS A 166 REMARK 465 ARG A 167 REMARK 465 ALA A 168 REMARK 465 ARG B 167 REMARK 465 ALA B 168 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC37838.3 RELATED DB: TARGETDB DBREF 3KKB A 42 168 UNP Q9HT87 Q9HT87_PSEAE 42 168 DBREF 3KKB B 42 168 UNP Q9HT87 Q9HT87_PSEAE 42 168 SEQADV 3KKB SER A 39 UNP Q9HT87 EXPRESSION TAG SEQADV 3KKB ASN A 40 UNP Q9HT87 EXPRESSION TAG SEQADV 3KKB ALA A 41 UNP Q9HT87 EXPRESSION TAG SEQADV 3KKB SER B 39 UNP Q9HT87 EXPRESSION TAG SEQADV 3KKB ASN B 40 UNP Q9HT87 EXPRESSION TAG SEQADV 3KKB ALA B 41 UNP Q9HT87 EXPRESSION TAG SEQRES 1 A 130 SER ASN ALA GLN GLU GLN ARG MSE SER HIS HIS TYR ALA SEQRES 2 A 130 THR ILE GLU VAL SER GLN GLN LEU ARG GLN LEU LEU GLY SEQRES 3 A 130 ASP GLN LEU VAL ILE LEU LEU ARG GLU THR PRO ASP GLY SEQRES 4 A 130 GLN ALA LEU GLU ARG SER GLN ASN ASP PHE ARG ARG VAL SEQRES 5 A 130 LEU GLU GLN GLY ARG ALA ASN THR VAL ASP SER ALA GLU SEQRES 6 A 130 GLN ALA ALA LEU ASP GLY VAL ARG ASP ALA TYR LEU GLN SEQRES 7 A 130 LEU GLN ALA HIS THR PRO ALA LEU LEU GLU ALA PRO MSE SEQRES 8 A 130 ALA ASP ASN ASP GLY PHE SER GLU ALA PHE ASN GLY LEU SEQRES 9 A 130 ARG LEU ARG LEU GLN ASP LEU GLN GLN LEU ALA LEU ALA SEQRES 10 A 130 GLY ILE SER GLU ALA GLU THR SER ALA ARG HIS ARG ALA SEQRES 1 B 130 SER ASN ALA GLN GLU GLN ARG MSE SER HIS HIS TYR ALA SEQRES 2 B 130 THR ILE GLU VAL SER GLN GLN LEU ARG GLN LEU LEU GLY SEQRES 3 B 130 ASP GLN LEU VAL ILE LEU LEU ARG GLU THR PRO ASP GLY SEQRES 4 B 130 GLN ALA LEU GLU ARG SER GLN ASN ASP PHE ARG ARG VAL SEQRES 5 B 130 LEU GLU GLN GLY ARG ALA ASN THR VAL ASP SER ALA GLU SEQRES 6 B 130 GLN ALA ALA LEU ASP GLY VAL ARG ASP ALA TYR LEU GLN SEQRES 7 B 130 LEU GLN ALA HIS THR PRO ALA LEU LEU GLU ALA PRO MSE SEQRES 8 B 130 ALA ASP ASN ASP GLY PHE SER GLU ALA PHE ASN GLY LEU SEQRES 9 B 130 ARG LEU ARG LEU GLN ASP LEU GLN GLN LEU ALA LEU ALA SEQRES 10 B 130 GLY ILE SER GLU ALA GLU THR SER ALA ARG HIS ARG ALA MODRES 3KKB MSE A 46 MET SELENOMETHIONINE MODRES 3KKB MSE A 129 MET SELENOMETHIONINE MODRES 3KKB MSE B 46 MET SELENOMETHIONINE MODRES 3KKB MSE B 129 MET SELENOMETHIONINE HET MSE A 46 8 HET MSE A 129 8 HET MSE B 46 8 HET MSE B 129 8 HET PO4 A 1 5 HET PO4 B 2 5 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *181(H2 O) HELIX 1 1 SER A 39 LEU A 71 1 33 HELIX 2 2 ASP A 76 THR A 98 1 23 HELIX 3 3 ASP A 100 ALA A 119 1 20 HELIX 4 4 HIS A 120 ALA A 127 1 8 HELIX 5 5 ASP A 133 SER A 163 1 31 HELIX 6 6 SER B 39 ARG B 72 1 34 HELIX 7 7 ASP B 76 THR B 98 1 23 HELIX 8 8 ASP B 100 HIS B 120 1 21 HELIX 9 9 ASP B 131 ARG B 165 1 35 LINK C ARG A 45 N MSE A 46 1555 1555 1.33 LINK C MSE A 46 N SER A 47 1555 1555 1.33 LINK C PRO A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N ALA A 130 1555 1555 1.33 LINK C ARG B 45 N MSE B 46 1555 1555 1.33 LINK C MSE B 46 N SER B 47 1555 1555 1.33 LINK C PRO B 128 N MSE B 129 1555 1555 1.33 LINK C MSE B 129 N ALA B 130 1555 1555 1.33 SITE 1 AC1 7 ARG A 60 HOH A 189 HOH A 202 HOH A 212 SITE 2 AC1 7 ARG B 60 ARG B 143 LEU B 146 SITE 1 AC2 5 ARG A 45 HOH A 229 ARG B 95 SER B 163 SITE 2 AC2 5 HOH B 193 CRYST1 75.361 75.361 75.020 90.00 90.00 120.00 P 32 2 1 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 0.013269 0.007661 0.000000 0.00000 SCALE2 0.000000 0.015322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013330 0.00000 MASTER 245 0 6 9 0 0 4 6 0 0 0 20 END