HEADER LYASE 16-JUN-09 3HVW TITLE CRYSTAL STRUCTURE OF THE GGDEF DOMAIN OF THE PA2567 PROTEIN FROM TITLE 2 PSEUDOMONAS AERUGINOSA, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET PAR365C COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIGUANYLATE-CYCLASE (DGC); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GGDEF DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: PA2567; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET 21-23C; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS ALPHA-BETA PROTEIN., STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,S.LEW,J.SEETHARAMAN,S.SAHDEV,R.XIAO,C.CICCOSANTI, AUTHOR 2 E.L.FOOTE,H.WANG,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST,G.T.MONTELIONE, AUTHOR 3 J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 06-NOV-24 3HVW 1 SEQADV REVDAT 3 24-JUL-19 3HVW 1 REMARK LINK REVDAT 2 01-NOV-17 3HVW 1 REMARK REVDAT 1 23-JUN-09 3HVW 0 JRNL AUTH F.FOROUHAR,S.LEW,J.SEETHARAMAN,S.SAHDEV,R.XIAO,C.CICCOSANTI, JRNL AUTH 2 E.L.FOOTE,H.WANG,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST, JRNL AUTH 3 G.T.MONTELIONE,J.F.HUNT,L.TONG JRNL TITL NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET PAR365C JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 & XTALVIEW REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1081506.375 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 42442 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2143 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3974 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 208 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.97000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -2.41000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.03 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 69.18 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053645. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97903 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43035 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : 0.02700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 49.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.07800 REMARK 200 R SYM FOR SHELL (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 23.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB THEN SOLVE/RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5), RESERVOIR SOLUTION: 100MM REMARK 280 TRIS (PH 8) AND 800MM AMMONIUM SULFATE, MICROBATCH, UNDER OIL, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 24.68700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.39600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.87850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.39600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.87850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 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 MSE A 167 REMARK 465 ILE A 168 REMARK 465 ASP A 169 REMARK 465 GLU A 170 REMARK 465 PRO A 171 REMARK 465 THR A 172 REMARK 465 GLY A 173 REMARK 465 LEU A 174 REMARK 465 ARG A 334 REMARK 465 LEU A 335 REMARK 465 GLU A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 REMARK 465 HIS A 342 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PAR365C RELATED DB: TARGETDB DBREF 3HVW A 168 334 UNP Q9I0R8 Q9I0R8_PSEAE 168 334 SEQADV 3HVW MSE A 167 UNP Q9I0R8 INITIATING METHIONINE SEQADV 3HVW LEU A 335 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW GLU A 336 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW HIS A 337 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW HIS A 338 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW HIS A 339 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW HIS A 340 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW HIS A 341 UNP Q9I0R8 EXPRESSION TAG SEQADV 3HVW HIS A 342 UNP Q9I0R8 EXPRESSION TAG SEQRES 1 A 176 MSE ILE ASP GLU PRO THR GLY LEU TYR ASN ARG LEU ARG SEQRES 2 A 176 LEU GLN GLU ASP VAL SER LEU ARG LEU GLN ARG ASP GLY SEQRES 3 A 176 ALA LEU THR VAL ILE ALA ALA ASP LEU LEU PRO LEU ALA SEQRES 4 A 176 LEU LEU ASN THR ILE ILE ARG THR LEU GLY TYR PRO PHE SEQRES 5 A 176 SER ASN ASP LEU MSE LEU GLU ALA ARG ASP ARG ILE ARG SEQRES 6 A 176 ALA GLU LEU PRO ASP PHE THR LEU TYR LYS ILE SER PRO SEQRES 7 A 176 THR ARG PHE GLY LEU LEU LEU PRO ARG GLN GLN GLN GLU SEQRES 8 A 176 GLU THR GLU SER VAL CYS LEU ARG LEU LEU ARG ALA PHE SEQRES 9 A 176 GLU SER PRO VAL VAL CYS ARG GLY ILE PRO ILE LYS ALA SEQRES 10 A 176 ASN VAL GLY LEU GLY VAL LEU PRO LEU ALA ASP ASP THR SEQRES 11 A 176 LEU ASP GLY ASP GLN ASP TRP LEU ARG LEU VAL VAL SER SEQRES 12 A 176 ALA ALA ASP ASP ALA ARG ASP ARG GLY VAL GLY TRP ALA SEQRES 13 A 176 ARG TYR ASN PRO PRO LEU ASP GLN ALA GLN GLN ARG LEU SEQRES 14 A 176 GLU HIS HIS HIS HIS HIS HIS MODRES 3HVW MSE A 223 MET SELENOMETHIONINE HET MSE A 223 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *235(H2 O) HELIX 1 1 ASN A 176 GLY A 192 1 17 HELIX 2 2 PRO A 203 GLY A 215 1 13 HELIX 3 3 GLY A 215 LEU A 234 1 20 HELIX 4 4 GLN A 254 GLU A 257 5 4 HELIX 5 5 GLU A 258 PHE A 270 1 13 HELIX 6 6 ASP A 295 GLN A 301 5 7 HELIX 7 7 TRP A 303 GLY A 318 1 16 SHEET 1 A 5 LEU A 239 SER A 243 0 SHEET 2 A 5 ARG A 246 PRO A 252 -1 O GLY A 248 N TYR A 240 SHEET 3 A 5 ALA A 193 ASP A 200 -1 N THR A 195 O LEU A 251 SHEET 4 A 5 GLY A 286 ALA A 293 -1 O GLY A 286 N ASP A 200 SHEET 5 A 5 ALA A 322 ARG A 323 1 O ALA A 322 N VAL A 289 SHEET 1 B 2 VAL A 274 CYS A 276 0 SHEET 2 B 2 ILE A 279 ILE A 281 -1 O ILE A 281 N VAL A 274 LINK C LEU A 222 N MSE A 223 1555 1555 1.33 LINK C MSE A 223 N LEU A 224 1555 1555 1.33 CRYST1 49.374 53.757 76.792 90.00 90.00 90.00 P 21 21 21 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 0.020254 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013022 0.00000