HEADER HYDROLASE 21-AUG-03 1UKF TITLE CRYSTAL STRUCTURE OF PSEUDOMONAS AVIRULENCE PROTEIN AVRPPHB COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVIRULENCE PROTEIN AVRPPH3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 81-267; COMPND 5 SYNONYM: PSEUDOMONAS AVRPPHB; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA; SOURCE 3 ORGANISM_TAXID: 319; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS AVRPPHB, AVRPPH3, AVIRULENCE, HYPERSENSITIVE RESPONSE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ZHU,F.SHAO,R.W.INNES,J.E.DIXON,Z.XU REVDAT 4 27-DEC-23 1UKF 1 SEQADV REVDAT 3 24-FEB-09 1UKF 1 VERSN REVDAT 2 13-JAN-04 1UKF 1 JRNL REVDAT 1 09-DEC-03 1UKF 0 JRNL AUTH M.ZHU,F.SHAO,R.W.INNES,J.E.DIXON,Z.XU JRNL TITL THE CRYSTAL STRUCTURE OF PSEUDOMONAS AVIRULENCE PROTEIN JRNL TITL 2 AVRPPHB: A PAPAIN-LIKE FOLD WITH A DISTINCT JRNL TITL 3 SUBSTRATE-BINDING SITE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 302 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 14694194 JRNL DOI 10.1073/PNAS.2036536100 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1053609.620 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 35498 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) : 0.204 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3553 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4876 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 552 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : -0.84000 REMARK 3 B33 (A**2) : -0.19000 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) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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 : 0.42 REMARK 3 BSOL : 62.03 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UKF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000005925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 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) : 0.9792, 0.9879, 0.9793, 0.9565 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39746 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : 0.03500 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PIPES, PH 6.7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K 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 21.80050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.85250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.79800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.85250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.80050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.79800 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 ARG A 205 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 208 CG OD1 ND2 REMARK 470 GLN A 242 CG CD OE1 NE2 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 90 119.32 -172.38 REMARK 500 SER A 179 104.49 -53.52 REMARK 500 ALA A 194 59.14 -91.08 REMARK 500 ALA A 207 -32.49 -35.43 REMARK 500 ASN A 208 43.35 -83.09 REMARK 500 VAL A 209 2.31 47.80 REMARK 500 ASN A 255 30.52 71.56 REMARK 500 TYR A 256 72.86 -115.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 1UKF A 81 267 UNP Q52430 AVRP3_PSESH 81 267 SEQADV 1UKF VAL A 268 UNP Q52430 EXPRESSION TAG SEQRES 1 A 188 SER LEU SER ASP PHE SER VAL ALA SER ARG ASP VAL ASN SEQRES 2 A 188 HIS ASN ASN ILE CYS ALA GLY LEU SER THR GLU TRP LEU SEQRES 3 A 188 VAL MET SER SER ASP GLY ASP ALA GLU SER ARG MET ASP SEQRES 4 A 188 HIS LEU ASP TYR ASN GLY GLU GLY GLN SER ARG GLY SER SEQRES 5 A 188 GLU ARG HIS GLN VAL TYR ASN ASP ALA LEU ARG ALA ALA SEQRES 6 A 188 LEU SER ASN ASP ASP GLU ALA PRO PHE PHE THR ALA SER SEQRES 7 A 188 THR ALA VAL ILE GLU ASP ALA GLY PHE SER LEU ARG ARG SEQRES 8 A 188 GLU PRO LYS THR VAL HIS ALA SER GLY GLY SER ALA GLN SEQRES 9 A 188 LEU GLY GLN THR VAL ALA HIS ASP VAL ALA GLN SER GLY SEQRES 10 A 188 ARG LYS HIS LEU LEU SER LEU ARG PHE ALA ASN VAL GLN SEQRES 11 A 188 GLY HIS ALA ILE ALA CYS SER CYS GLU GLY SER GLN PHE SEQRES 12 A 188 LYS LEU PHE ASP PRO ASN LEU GLY GLU PHE GLN SER SER SEQRES 13 A 188 ARG SER ALA ALA PRO GLN LEU ILE LYS GLY LEU ILE ASP SEQRES 14 A 188 HIS TYR ASN SER LEU ASN TYR ASP VAL ALA CYS VAL ASN SEQRES 15 A 188 GLU PHE ARG VAL SER VAL FORMUL 2 HOH *197(H2 O) HELIX 1 1 SER A 81 ASP A 84 5 4 HELIX 2 2 ILE A 97 MET A 108 1 12 HELIX 3 3 ASP A 113 ASP A 122 1 10 HELIX 4 4 GLY A 125 ASN A 148 1 24 HELIX 5 5 ALA A 152 ALA A 165 1 14 HELIX 6 6 GLY A 181 ALA A 194 1 14 HELIX 7 7 ALA A 239 LEU A 254 1 16 SHEET 1 A 7 SER A 86 SER A 89 0 SHEET 2 A 7 GLY A 231 SER A 236 -1 O GLU A 232 N ALA A 88 SHEET 3 A 7 GLN A 222 ASP A 227 -1 N LEU A 225 O PHE A 233 SHEET 4 A 7 GLN A 210 GLU A 219 -1 N ALA A 215 O PHE A 226 SHEET 5 A 7 LYS A 199 PHE A 206 -1 N LEU A 202 O ILE A 214 SHEET 6 A 7 VAL A 258 SER A 267 -1 O ASN A 262 N SER A 203 SHEET 7 A 7 SER A 168 LEU A 169 -1 N SER A 168 O SER A 267 SHEET 1 B 7 SER A 86 SER A 89 0 SHEET 2 B 7 GLY A 231 SER A 236 -1 O GLU A 232 N ALA A 88 SHEET 3 B 7 GLN A 222 ASP A 227 -1 N LEU A 225 O PHE A 233 SHEET 4 B 7 GLN A 210 GLU A 219 -1 N ALA A 215 O PHE A 226 SHEET 5 B 7 LYS A 199 PHE A 206 -1 N LEU A 202 O ILE A 214 SHEET 6 B 7 VAL A 258 SER A 267 -1 O ASN A 262 N SER A 203 SHEET 7 B 7 LYS A 174 HIS A 177 -1 N LYS A 174 O GLU A 263 CRYST1 43.601 49.596 75.705 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 0.022935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013209 0.00000