HEADER TRANSFERASE 15-JUN-09 3HVA TITLE CRYSTAL STRUCTURE OF FIMX GGDEF DOMAIN FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FIMX; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: GGDEF DOMAIN: UNP RESIDUES 260-431; COMPND 5 EC: 2.7.7.65; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1 / 1C / PRS 101 / LMG 12228; SOURCE 5 ATCC: 15692; SOURCE 6 GENE: FIMX, PA4959; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPSUMO KEYWDS GGDEF DIGUANYLATE CYCLASE, BIOFILM, C-DI-GMP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.V.A.S.NAVARRO,N.DE,N.BAE,H.SONDERMANN REVDAT 3 06-SEP-23 3HVA 1 SEQADV REVDAT 2 21-MAR-12 3HVA 1 JRNL VERSN REVDAT 1 18-AUG-09 3HVA 0 JRNL AUTH M.V.NAVARRO,N.DE,N.BAE,Q.WANG,H.SONDERMANN JRNL TITL STRUCTURAL ANALYSIS OF THE GGDEF-EAL DOMAIN-CONTAINING JRNL TITL 2 C-DI-GMP RECEPTOR FIMX. JRNL REF STRUCTURE V. 17 1104 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19679088 JRNL DOI 10.1016/J.STR.2009.06.010 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 16711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 881 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 27.1180 - 4.0797 0.98 2117 108 0.1750 0.2114 REMARK 3 2 4.0797 - 3.2399 0.98 2078 122 0.1691 0.2040 REMARK 3 3 3.2399 - 2.8309 0.98 2071 98 0.2252 0.2914 REMARK 3 4 2.8309 - 2.5723 0.98 2055 90 0.2415 0.2826 REMARK 3 5 2.5723 - 2.3880 0.98 1972 113 0.2583 0.2462 REMARK 3 6 2.3880 - 2.2473 0.98 1982 106 0.2646 0.2971 REMARK 3 7 2.2473 - 2.1348 0.98 1925 113 0.2576 0.2908 REMARK 3 8 2.1348 - 2.0420 0.98 1660 101 0.2705 0.2836 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 : 0.39 REMARK 3 B_SOL : 43.25 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL 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: 0.1910 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 NULL REMARK 3 ANGLE : 0.723 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 3HVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9771 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17415 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.17400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.400 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: PDB ENTRY 1W25 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME 5000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 47.05550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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: MONOMERIC 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLY A 255 REMARK 465 ALA A 256 REMARK 465 MET A 257 REMARK 465 GLY A 258 REMARK 465 SER A 259 REMARK 465 GLU A 260 REMARK 465 GLU A 261 REMARK 465 LYS A 262 REMARK 465 LEU A 263 REMARK 465 ARG A 264 REMARK 465 GLU A 265 REMARK 465 TYR A 428 REMARK 465 ASN A 429 REMARK 465 PRO A 430 REMARK 465 ALA A 431 REMARK 465 GLY B 255 REMARK 465 ALA B 256 REMARK 465 MET B 257 REMARK 465 GLY B 258 REMARK 465 SER B 259 REMARK 465 GLU B 260 REMARK 465 GLU B 261 REMARK 465 LYS B 262 REMARK 465 LEU B 263 REMARK 465 ARG B 264 REMARK 465 GLU B 265 REMARK 465 TYR B 428 REMARK 465 ASN B 429 REMARK 465 PRO B 430 REMARK 465 ALA B 431 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HV8 RELATED DB: PDB REMARK 900 FIMX EAL DOMAIN C-DI-GMP BOUND REMARK 900 RELATED ID: 3HV9 RELATED DB: PDB REMARK 900 FIMX EAL DOMAIN C-DI-GMP FREE REMARK 900 RELATED ID: 3HVB RELATED DB: PDB REMARK 900 FIMX DUAL-DOMAIN GGDEF-EAL MODULE DBREF 3HVA A 260 431 UNP Q9HUK6 Q9HUK6_PSEAE 260 431 DBREF 3HVA B 260 431 UNP Q9HUK6 Q9HUK6_PSEAE 260 431 SEQADV 3HVA GLY A 255 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA ALA A 256 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA MET A 257 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA GLY A 258 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA SER A 259 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA GLY B 255 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA ALA B 256 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA MET B 257 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA GLY B 258 UNP Q9HUK6 EXPRESSION TAG SEQADV 3HVA SER B 259 UNP Q9HUK6 EXPRESSION TAG SEQRES 1 A 177 GLY ALA MET GLY SER GLU GLU LYS LEU ARG GLU VAL SER SEQRES 2 A 177 SER GLN ASP PRO VAL THR GLY LEU TYR ASN ARG SER HIS SEQRES 3 A 177 PHE LEU ASP LEU MET ASP ALA ALA VAL GLN GLN ALA VAL SEQRES 4 A 177 THR ALA ARG LYS PRO SER THR LEU ALA TYR ILE HIS LEU SEQRES 5 A 177 ASN GLY TYR PRO SER LEU GLN ALA ASP HIS GLY LEU SER SEQRES 6 A 177 GLY ILE ASP LEU LEU LEU GLY GLN LEU ALA GLY LEU MET SEQRES 7 A 177 ARG GLU GLN PHE GLY GLU GLU ALA ASP LEU ALA ARG PHE SEQRES 8 A 177 GLY ASP SER ILE PHE ALA ALA LEU PHE LYS GLY LYS THR SEQRES 9 A 177 PRO GLU GLN ALA GLN ALA ALA LEU GLN ARG LEU LEU LYS SEQRES 10 A 177 LYS VAL GLU ASN HIS LEU PHE GLU LEU ASN GLY ARG SER SEQRES 11 A 177 ALA GLN ALA THR LEU SER ILE GLY VAL ALA GLY LEU ASP SEQRES 12 A 177 GLU LYS THR ALA LYS ALA GLN ASP VAL MET ASN ARG ALA SEQRES 13 A 177 HIS ARG CYS ALA ASP ASP ALA ALA ARG LYS GLY GLY SER SEQRES 14 A 177 GLN ILE LYS GLN TYR ASN PRO ALA SEQRES 1 B 177 GLY ALA MET GLY SER GLU GLU LYS LEU ARG GLU VAL SER SEQRES 2 B 177 SER GLN ASP PRO VAL THR GLY LEU TYR ASN ARG SER HIS SEQRES 3 B 177 PHE LEU ASP LEU MET ASP ALA ALA VAL GLN GLN ALA VAL SEQRES 4 B 177 THR ALA ARG LYS PRO SER THR LEU ALA TYR ILE HIS LEU SEQRES 5 B 177 ASN GLY TYR PRO SER LEU GLN ALA ASP HIS GLY LEU SER SEQRES 6 B 177 GLY ILE ASP LEU LEU LEU GLY GLN LEU ALA GLY LEU MET SEQRES 7 B 177 ARG GLU GLN PHE GLY GLU GLU ALA ASP LEU ALA ARG PHE SEQRES 8 B 177 GLY ASP SER ILE PHE ALA ALA LEU PHE LYS GLY LYS THR SEQRES 9 B 177 PRO GLU GLN ALA GLN ALA ALA LEU GLN ARG LEU LEU LYS SEQRES 10 B 177 LYS VAL GLU ASN HIS LEU PHE GLU LEU ASN GLY ARG SER SEQRES 11 B 177 ALA GLN ALA THR LEU SER ILE GLY VAL ALA GLY LEU ASP SEQRES 12 B 177 GLU LYS THR ALA LYS ALA GLN ASP VAL MET ASN ARG ALA SEQRES 13 B 177 HIS ARG CYS ALA ASP ASP ALA ALA ARG LYS GLY GLY SER SEQRES 14 B 177 GLN ILE LYS GLN TYR ASN PRO ALA FORMUL 3 HOH *143(H2 O) HELIX 1 1 ARG A 278 ALA A 295 1 18 HELIX 2 2 GLY A 308 GLY A 337 1 30 HELIX 3 3 GLU A 338 ALA A 340 5 3 HELIX 4 4 THR A 358 ASN A 375 1 18 HELIX 5 5 LYS A 402 ARG A 419 1 18 HELIX 6 6 ARG B 278 ALA B 295 1 18 HELIX 7 7 GLY B 308 GLY B 337 1 30 HELIX 8 8 THR B 358 HIS B 376 1 19 HELIX 9 9 LYS B 402 GLY B 421 1 20 SHEET 1 A 6 TYR A 276 ASN A 277 0 SHEET 2 A 6 ASP A 341 ARG A 344 1 O ARG A 344 N TYR A 276 SHEET 3 A 6 ILE A 349 LYS A 355 -1 O ALA A 351 N ALA A 343 SHEET 4 A 6 SER A 299 LEU A 306 -1 N ALA A 302 O ALA A 352 SHEET 5 A 6 LEU A 389 LEU A 396 -1 O GLY A 392 N TYR A 303 SHEET 6 A 6 GLN A 424 LYS A 426 1 O GLN A 424 N ILE A 391 SHEET 1 B 2 PHE A 378 LEU A 380 0 SHEET 2 B 2 ARG A 383 ALA A 385 -1 O ARG A 383 N LEU A 380 SHEET 1 C 6 TYR B 276 ASN B 277 0 SHEET 2 C 6 ALA B 340 ARG B 344 1 O ARG B 344 N TYR B 276 SHEET 3 C 6 ILE B 349 LYS B 355 -1 O ALA B 351 N ALA B 343 SHEET 4 C 6 SER B 299 LEU B 306 -1 N THR B 300 O PHE B 354 SHEET 5 C 6 LEU B 389 LEU B 396 -1 O SER B 390 N HIS B 305 SHEET 6 C 6 GLN B 424 LYS B 426 1 O LYS B 426 N ILE B 391 SHEET 1 D 2 PHE B 378 GLU B 379 0 SHEET 2 D 2 SER B 384 ALA B 385 -1 O ALA B 385 N PHE B 378 CRYST1 33.179 94.111 45.504 90.00 90.61 90.00 P 1 21 1 4 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 0.030140 0.000000 0.000324 0.00000 SCALE2 0.000000 0.010626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021977 0.00000