HEADER CHAPERONE 07-JAN-04 1S21 TITLE CRYSTAL STRUCTURE OF AVRPPHF ORF2, A TYPE III EFFECTOR FROM P. TITLE 2 SYRINGAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AVRPPHF ORF2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA; SOURCE 3 ORGANISM_TAXID: 319; SOURCE 4 GENE: AVRPPHF ORF2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 RIL CODON PLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTA KEYWDS PREDOMINANTLY BETA-STRAND, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR A.U.SINGER,D.DESVEAUX,L.BETTS,J.H.CHANG,Z.NIMCHUK,S.R.GRANT, AUTHOR 2 J.K.DANGL,J.SONDEK REVDAT 4 14-FEB-24 1S21 1 SEQADV REVDAT 3 11-OCT-17 1S21 1 REMARK REVDAT 2 24-FEB-09 1S21 1 VERSN REVDAT 1 14-SEP-04 1S21 0 JRNL AUTH A.U.SINGER,D.DESVEAUX,L.BETTS,J.H.CHANG,Z.NIMCHUK,S.R.GRANT, JRNL AUTH 2 J.K.DANGL,J.SONDEK JRNL TITL CRYSTAL STRUCTURES OF THE TYPE III EFFECTOR PROTEIN AVRPPHF JRNL TITL 2 AND ITS CHAPERONE REVEAL RESIDUES REQUIRED FOR PLANT JRNL TITL 3 PATHOGENESIS JRNL REF STRUCTURE V. 12 1669 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15341731 JRNL DOI 10.1016/J.STR.2004.06.023 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1137637.670 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 16408 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) : 0.225 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 798 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2553 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 116 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1267 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.36000 REMARK 3 B22 (A**2) : -2.49000 REMARK 3 B33 (A**2) : -6.87000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 1.030 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.390 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 41.16 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_REP.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 1S21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-02; 26-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N REMARK 200 RADIATION SOURCE : ROTATING ANODE; NULL REMARK 200 BEAMLINE : NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : OSMIC CONFOCAL "BLUE" OPTICS; REMARK 200 OSMIC CONFOCAL "BLUE" OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++; RIGAKU RAXIS REMARK 200 IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16442 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, BIS-TRIS, MAGNESIUM ACETATE REMARK 280 AND GLYCEROL, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K. AMMONIUM SULFATE, PEG400, HEPES AND GLYCEROL, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 19.34450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.18250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.16700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.18250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.34450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.16700 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 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 -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 CYS A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 GLY A 9 REMARK 465 VAL A 10 REMARK 465 SER A 11 REMARK 465 ARG A 12 REMARK 465 THR A 13 REMARK 465 TYR A 14 REMARK 465 SER A 15 REMARK 465 PRO A 16 REMARK 465 PRO A 17 REMARK 465 THR A 18 REMARK 465 SER A 19 REMARK 465 PRO A 20 REMARK 465 VAL A 21 REMARK 465 TYR A 22 REMARK 465 GLY A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 VAL A 26 REMARK 465 SER A 27 REMARK 465 SER A 28 REMARK 465 ARG A 147 REMARK 465 GLY A 148 REMARK 465 TYR A 149 REMARK 465 ALA A 150 REMARK 465 GLY A 151 REMARK 465 SER A 152 REMARK 465 ASP A 153 REMARK 465 ALA A 177 REMARK 465 MET A 178 REMARK 465 SER A 179 REMARK 465 ALA A 180 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 LEU A 146 O REMARK 470 HIS A 154 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 176 O 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 THR A 74 -165.62 -160.38 REMARK 500 PRO A 193 144.64 -37.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 1S21 A 1 204 UNP Q9K2L5 Q9K2L5_PSESH 1 204 SEQADV 1S21 GLY A -1 UNP Q9K2L5 CLONING ARTIFACT SEQADV 1S21 ALA A 0 UNP Q9K2L5 CLONING ARTIFACT SEQRES 1 A 206 GLY ALA MET GLY ASN ILE CYS ASN SER GLY GLY VAL SER SEQRES 2 A 206 ARG THR TYR SER PRO PRO THR SER PRO VAL TYR GLY SER SEQRES 3 A 206 GLY VAL SER SER PRO SER ARG PHE VAL GLY GLN TYR THR SEQRES 4 A 206 LEU THR SER ILE HIS GLN LEU SER SER GLU GLU ARG GLU SEQRES 5 A 206 ASN PHE LEU ASP ALA HIS ASP PRO MET ARG VAL TYR ASP SEQRES 6 A 206 LEU ASN SER GLU THR SER VAL TYR ARG THR THR GLN ARG SEQRES 7 A 206 GLU TYR VAL ARG ASN GLY TYR ALA THR GLY ASN PRO ASN SEQRES 8 A 206 SER GLY ALA ILE ILE ALA LEU HIS GLU GLU LEU GLN GLU SEQRES 9 A 206 SER PRO TYR ALA GLN HIS ILE GLY ALA ARG PRO ASP GLN SEQRES 10 A 206 ALA ASP ALA TYR ARG PRO ARG THR ALA HIS VAL SER SER SEQRES 11 A 206 LEU ASN THR PRO SER LEU ASN VAL MET ALA GLY GLN GLY SEQRES 12 A 206 ALA LEU SER ALA LEU ARG GLY TYR ALA GLY SER ASP HIS SEQRES 13 A 206 VAL THR THR GLU MET ARG LEU GLY ASP PHE LEU ASP GLN SEQRES 14 A 206 GLY GLY LYS VAL TYR SER ASP THR SER ALA MET SER ALA SEQRES 15 A 206 GLY GLY ASP SER VAL GLU ALA LEU ILE VAL THR LEU PRO SEQRES 16 A 206 LYS GLY ARG LYS VAL PRO VAL ASN ILE LEU ASP FORMUL 2 HOH *145(H2 O) HELIX 1 1 SER A 40 LEU A 44 5 5 HELIX 2 2 SER A 45 ASP A 57 1 13 HELIX 3 3 ASP A 57 TYR A 62 1 6 HELIX 4 4 GLN A 75 ARG A 80 1 6 HELIX 5 5 GLN A 115 ASP A 117 5 3 HELIX 6 6 SER A 127 ASN A 130 5 4 HELIX 7 7 GLY A 141 LEU A 146 1 6 HELIX 8 8 LEU A 161 ASP A 166 1 6 SHEET 1 A 3 SER A 69 THR A 74 0 SHEET 2 A 3 VAL A 155 ARG A 160 -1 O VAL A 155 N THR A 74 SHEET 3 A 3 ASN A 201 ILE A 202 -1 O ASN A 201 N GLU A 158 SHEET 1 B 2 TYR A 83 THR A 85 0 SHEET 2 B 2 LYS A 197 PRO A 199 -1 O VAL A 198 N ALA A 84 SHEET 1 C 2 ILE A 93 GLU A 102 0 SHEET 2 C 2 TYR A 119 HIS A 125 -1 O ARG A 122 N LEU A 96 SHEET 1 D 3 SER A 133 ALA A 138 0 SHEET 2 D 3 GLU A 186 THR A 191 -1 O LEU A 188 N VAL A 136 SHEET 3 D 3 VAL A 171 SER A 173 -1 N TYR A 172 O ILE A 189 CRYST1 38.689 68.334 88.365 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 0.025847 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011317 0.00000