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