HEADER CELL INVASION 20-MAR-07 2P7N TITLE CRYSTAL STRUCTURE OF THE PATHOGENICITY ISLAND 1 EFFECTOR PROTEIN FROM TITLE 2 CHROMOBACTERIUM VIOLACEUM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 (NESGC) TARGET CVR69. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PATHOGENICITY ISLAND 1 EFFECTOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHROMOBACTERIUM VIOLACEUM; SOURCE 3 ORGANISM_TAXID: 536; SOURCE 4 STRAIN: DSM 30191, IFO 12614, JCM 1249, NCIB 9131; SOURCE 5 ATCC: 12472; SOURCE 6 GENE: SIPD, CV_2617; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS CVR69, PATHOGENICITY ISLAND 1 EFFECTOR PROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, CELL INVASION EXPDTA X-RAY DIFFRACTION AUTHOR J.BENACH,M.ABASHIDZE,J.SEETHARAMAN,L.ZHAO,H.JANJUA,K.CUNNINGHAM, AUTHOR 2 L.C.MA,R.XIAO,J.LIU,M.C.BARAN,T.B.ACTON,B.ROST,G.T.MONTELIONE, AUTHOR 3 J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 18-OCT-17 2P7N 1 REMARK REVDAT 2 24-FEB-09 2P7N 1 VERSN REVDAT 1 03-APR-07 2P7N 0 JRNL AUTH J.BENACH,M.ABASHIDZE,J.SEETHARAMAN,L.ZHAO,H.JANJUA, JRNL AUTH 2 K.CUNNINGHAM,L.C.MA,R.XIAO,J.LIU,M.C.BARAN,T.B.ACTON,B.ROST, JRNL AUTH 3 G.T.MONTELIONE,J.F.HUNT,L.TONG, JRNL AUTH 4 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) JRNL TITL CRYSTAL STRUCTURE OF THE PATHOGENICITY ISLAND 1 EFFECTOR JRNL TITL 2 PROTEIN FROM CHROMOBACTERIUM VIOLACEUM. NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS CONSORTIUM (NESGC) TARGET CVR69. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 485.00 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 15650 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1496 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 29 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 385 REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE : 0.5000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 31 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.02200 REMARK 3 B22 (A**2) : -19.06600 REMARK 3 B33 (A**2) : 25.08800 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.542 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.602 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.451 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.930 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 11.09 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.PAR REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL PAIRS WERE USED FOR PHASING REMARK 4 REMARK 4 2P7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912, 0.97897, 0.96862 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21495 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.66500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM SODIUM ACETATE PH 4.6, 22% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 27.51300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.49050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 97.39100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.51300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.49050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.39100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.51300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.49050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 97.39100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.51300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.49050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 97.39100 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: A DIMER CAN BE CONSTRUCTED BY APPLYING THE SYMMETRY REMARK 300 OPERATION (-X,-Y,Z) 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 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 BIOMT1 2 -1.000000 0.000000 0.000000 55.02600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 66.98100 REMARK 350 BIOMT3 2 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 1 REMARK 465 TYR A 2 REMARK 465 GLY A 3 REMARK 465 ILE A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 SER A 7 REMARK 465 ALA A 8 REMARK 465 SER A 9 REMARK 465 LEU A 10 REMARK 465 PRO A 11 REMARK 465 LEU A 12 REMARK 465 THR A 13 REMARK 465 ARG A 14 REMARK 465 PRO A 15 REMARK 465 GLN A 16 REMARK 465 ALA A 17 REMARK 465 LEU A 18 REMARK 465 GLU A 19 REMARK 465 THR A 20 REMARK 465 GLN A 21 REMARK 465 ALA A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 PRO A 25 REMARK 465 GLN A 26 REMARK 465 SER A 27 REMARK 465 ASP A 28 REMARK 465 ALA A 29 REMARK 465 PRO A 30 REMARK 465 ASP A 31 REMARK 465 ALA A 32 REMARK 465 SER A 33 REMARK 465 ALA A 34 REMARK 465 GLY A 35 REMARK 465 GLN A 36 REMARK 465 THR A 37 REMARK 465 ARG A 38 REMARK 465 ALA A 39 REMARK 465 ALA A 40 REMARK 465 PRO A 41 REMARK 465 GLN A 42 REMARK 465 GLY A 43 REMARK 465 SER A 44 REMARK 465 ALA A 45 REMARK 465 ALA A 46 REMARK 465 GLN A 96 REMARK 465 LYS A 226 REMARK 465 PRO A 227 REMARK 465 GLY A 228 REMARK 465 GLY A 229 REMARK 465 ASP A 230 REMARK 465 GLY A 231 REMARK 465 ASN A 232 REMARK 465 LYS A 233 REMARK 465 VAL A 234 REMARK 465 GLU A 335 REMARK 465 ALA A 393 REMARK 465 LYS A 394 REMARK 465 SER A 395 REMARK 465 PHE A 396 REMARK 465 LEU A 397 REMARK 465 GLN A 398 REMARK 465 ILE A 399 REMARK 465 LEU A 400 REMARK 465 GLU A 401 REMARK 465 HIS A 402 REMARK 465 HIS A 403 REMARK 465 HIS A 404 REMARK 465 HIS A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN A 195 CG2 VAL A 199 1.92 REMARK 500 O SER A 90 N GLY A 92 2.04 REMARK 500 O GLY A 328 N GLY A 331 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A 92 CA GLY A 92 C -0.109 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 107 N - CA - C ANGL. DEV. = 28.2 DEGREES REMARK 500 GLY A 331 CA - C - N ANGL. DEV. = -19.6 DEGREES REMARK 500 SER A 332 N - CA - C ANGL. DEV. = 20.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 48 23.58 -73.35 REMARK 500 PRO A 102 13.26 -49.52 REMARK 500 ASP A 107 -77.08 -50.18 REMARK 500 ARG A 110 9.24 -67.47 REMARK 500 ALA A 151 -72.20 -66.72 REMARK 500 PRO A 154 -174.68 -49.46 REMARK 500 ASN A 237 68.94 -106.59 REMARK 500 GLN A 276 91.18 -163.49 REMARK 500 ALA A 295 119.49 -30.49 REMARK 500 ALA A 307 8.58 -67.42 REMARK 500 SER A 332 -172.94 -60.30 REMARK 500 ASN A 340 7.43 -65.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 91 GLY A 92 -136.31 REMARK 500 GLY A 331 SER A 332 -125.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 91 -17.55 REMARK 500 GLY A 331 -22.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CVR69 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2JAA RELATED DB: PDB REMARK 900 SHIGELLA FLEXNERI IPAD DBREF 2P7N A 1 399 UNP Q7NUT0 Q7NUT0_CHRVO 1 399 SEQADV 2P7N MSE A 1 UNP Q7NUT0 MET 1 MODIFIED RESIDUE SEQADV 2P7N MSE A 134 UNP Q7NUT0 MET 134 MODIFIED RESIDUE SEQADV 2P7N MSE A 164 UNP Q7NUT0 MET 164 MODIFIED RESIDUE SEQADV 2P7N MSE A 176 UNP Q7NUT0 MET 176 MODIFIED RESIDUE SEQADV 2P7N MSE A 184 UNP Q7NUT0 MET 184 MODIFIED RESIDUE SEQADV 2P7N MSE A 221 UNP Q7NUT0 MET 221 MODIFIED RESIDUE SEQADV 2P7N MSE A 290 UNP Q7NUT0 MET 290 MODIFIED RESIDUE SEQADV 2P7N MSE A 317 UNP Q7NUT0 MET 317 MODIFIED RESIDUE SEQADV 2P7N MSE A 323 UNP Q7NUT0 MET 323 MODIFIED RESIDUE SEQADV 2P7N LEU A 400 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N GLU A 401 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N HIS A 402 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N HIS A 403 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N HIS A 404 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N HIS A 405 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N HIS A 406 UNP Q7NUT0 CLONING ARTIFACT SEQADV 2P7N HIS A 407 UNP Q7NUT0 CLONING ARTIFACT SEQRES 1 A 407 MSE TYR GLY ILE GLN THR SER ALA SER LEU PRO LEU THR SEQRES 2 A 407 ARG PRO GLN ALA LEU GLU THR GLN ALA ALA ALA PRO GLN SEQRES 3 A 407 SER ASP ALA PRO ASP ALA SER ALA GLY GLN THR ARG ALA SEQRES 4 A 407 ALA PRO GLN GLY SER ALA ALA PRO ALA LEU ALA ALA ALA SEQRES 5 A 407 ARG ALA LYS ALA ASP GLU LEU GLY GLN ALA ALA ARG GLU SEQRES 6 A 407 VAL ARG ALA SER VAL GLU ARG GLN THR ALA TYR GLU THR SEQRES 7 A 407 ARG LEU ALA ALA GLN ARG SER ALA ALA ALA PHE SER GLY SEQRES 8 A 407 GLY GLU PRO PRO GLN ALA ARG ARG GLU ALA PRO GLY ALA SEQRES 9 A 407 GLU LEU ASP GLU ALA ARG ASN ALA GLN THR VAL SER ALA SEQRES 10 A 407 ARG LEU PHE GLU GLY ASN LEU LYS GLY VAL ALA GLN SER SEQRES 11 A 407 GLY HIS ALA MSE SER ALA GLU GLN LYS GLN ALA LEU GLN SEQRES 12 A 407 SER GLY LEU ASP ASP VAL PHE ALA ASP ALA PRO PRO GLN SEQRES 13 A 407 ALA ARG SER ALA GLY ALA PRO MSE LEU TYR SER ALA ASN SEQRES 14 A 407 ALA ALA ALA GLY GLN GLY MSE ALA ASP SER ASP LEU TRP SEQRES 15 A 407 ASP MSE ILE SER ASP GLN ILE GLY LYS ILE LYS ASP ASN SEQRES 16 A 407 TYR LEU GLY VAL TYR GLU ASN VAL VAL GLY GLN TYR THR SEQRES 17 A 407 ASP PHE TYR LYS ALA PHE SER ASP ILE LEU SER GLN MSE SEQRES 18 A 407 ALA ASN TRP ILE LYS PRO GLY GLY ASP GLY ASN LYS VAL SEQRES 19 A 407 LYS LEU ASN VAL ASP ALA LEU LYS ALA ALA LEU GLU LYS SEQRES 20 A 407 LEU LYS LYS ASP PHE SER LEU GLY ASP ASN LEU ASP ASN SEQRES 21 A 407 LYS LYS ALA VAL LEU PHE PRO ALA GLN SER LYS ASP GLY SEQRES 22 A 407 GLY ILE GLN GLY GLY SER GLU SER ASP ALA ARG LYS TRP SEQRES 23 A 407 ALA LYS GLU MSE GLY LEU PRO ASP ALA PRO PRO PRO GLY SEQRES 24 A 407 PHE SER CYS VAL GLN LYS ALA ALA ASP GLY ASN TRP VAL SEQRES 25 A 407 VAL VAL VAL ASP MSE THR PRO ILE ASP THR MSE ILE ARG SEQRES 26 A 407 ASP VAL GLY ALA LEU GLY SER GLY THR GLU LEU GLU LEU SEQRES 27 A 407 ASP ASN ALA LYS PHE GLN ALA TRP GLN SER GLY PHE LYS SEQRES 28 A 407 ALA GLN GLU GLU ASN LEU LYS ASN THR LEU GLN THR LEU SEQRES 29 A 407 THR GLN LYS TYR SER ASN ALA ASN SER LEU PHE ASP ASN SEQRES 30 A 407 LEU VAL LYS VAL LEU SER SER THR ILE SER SER CYS LEU SEQRES 31 A 407 GLU THR ALA LYS SER PHE LEU GLN ILE LEU GLU HIS HIS SEQRES 32 A 407 HIS HIS HIS HIS MODRES 2P7N MSE A 134 MET SELENOMETHIONINE MODRES 2P7N MSE A 164 MET SELENOMETHIONINE MODRES 2P7N MSE A 176 MET SELENOMETHIONINE MODRES 2P7N MSE A 184 MET SELENOMETHIONINE MODRES 2P7N MSE A 221 MET SELENOMETHIONINE MODRES 2P7N MSE A 290 MET SELENOMETHIONINE MODRES 2P7N MSE A 317 MET SELENOMETHIONINE MODRES 2P7N MSE A 323 MET SELENOMETHIONINE HET MSE A 134 8 HET MSE A 164 8 HET MSE A 176 8 HET MSE A 184 8 HET MSE A 221 8 HET MSE A 290 8 HET MSE A 317 8 HET MSE A 323 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 HOH *15(H2 O) HELIX 1 1 ALA A 48 SER A 90 1 43 HELIX 2 2 GLU A 108 SER A 130 1 23 HELIX 3 3 SER A 135 ALA A 151 1 17 HELIX 4 4 PRO A 154 SER A 159 1 6 HELIX 5 5 GLY A 161 GLN A 174 1 14 HELIX 6 6 ALA A 177 TYR A 196 1 20 HELIX 7 7 TYR A 196 ALA A 222 1 27 HELIX 8 8 ASN A 223 ILE A 225 5 3 HELIX 9 9 ASN A 237 PHE A 252 1 16 HELIX 10 10 SER A 279 MSE A 290 1 12 HELIX 11 11 MSE A 317 LEU A 330 1 14 HELIX 12 12 LYS A 342 GLU A 391 1 50 SHEET 1 A 3 VAL A 264 PHE A 266 0 SHEET 2 A 3 TRP A 311 VAL A 314 -1 O VAL A 313 N LEU A 265 SHEET 3 A 3 VAL A 303 LYS A 305 -1 N GLN A 304 O VAL A 312 LINK C ALA A 133 N MSE A 134 1555 1555 1.33 LINK C MSE A 134 N SER A 135 1555 1555 1.38 LINK C PRO A 163 N MSE A 164 1555 1555 1.32 LINK C MSE A 164 N LEU A 165 1555 1555 1.33 LINK C GLY A 175 N MSE A 176 1555 1555 1.33 LINK C MSE A 176 N ALA A 177 1555 1555 1.33 LINK C ASP A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N ILE A 185 1555 1555 1.33 LINK C GLN A 220 N MSE A 221 1555 1555 1.33 LINK C MSE A 221 N ALA A 222 1555 1555 1.33 LINK C GLU A 289 N MSE A 290 1555 1555 1.33 LINK C MSE A 290 N GLY A 291 1555 1555 1.33 LINK C ASP A 316 N MSE A 317 1555 1555 1.33 LINK C MSE A 317 N THR A 318 1555 1555 1.33 LINK C THR A 322 N MSE A 323 1555 1555 1.33 LINK C MSE A 323 N ILE A 324 1555 1555 1.33 CISPEP 1 PHE A 266 PRO A 267 0 0.39 CISPEP 2 PRO A 297 PRO A 298 0 -2.35 CRYST1 55.026 66.981 194.782 90.00 90.00 90.00 I 2 2 2 8 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 0.018173 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005134 0.00000