HEADER PROTEIN TRANSPORT 09-SEP-08 2JLH TITLE CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF YERSINIA PESTIS YSCU TITLE 2 N263A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: YOP PROTEINS TRANSLOCATION PROTEIN U; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN, RESIDUES 211-354; COMPND 5 SYNONYM: YSCU; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PBA2086 KEYWDS CELL MEMBRANE, TRANSMEMBRANE, YERSINIA PESTIS, MOLECULAR SWITCH, KEYWDS 2 PROTEIN TRANSPORT, ATOMIC RESOLUTION, MEMBRANE, VIRULENCE, KEYWDS 3 TRANSPORT, TYPE III SECRETION SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR G.T.LOUNTOS,B.P.AUSTIN,S.NALLAMSETTY,D.S.WAUGH REVDAT 4 13-DEC-23 2JLH 1 REMARK REVDAT 3 13-JUL-11 2JLH 1 VERSN REVDAT 2 11-AUG-09 2JLH 1 JRNL REVDAT 1 03-FEB-09 2JLH 0 JRNL AUTH G.T.LOUNTOS,B.P.AUSTIN,S.NALLAMSETTY,D.S.WAUGH JRNL TITL ATOMIC RESOLUTION STRUCTURE OF THE CYTOPLASMIC DOMAIN OF JRNL TITL 2 YERSINIA PESTIS YSCU, A REGULATORY SWITCH INVOLVED IN TYPE JRNL TITL 3 III SECRETION. JRNL REF PROTEIN SCI. V. 18 467 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19165725 JRNL DOI 10.1002/PRO.56 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0057 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 21243 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 + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1144 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1485 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 907 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 0.44000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.075 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.510 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 982 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 697 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1324 ; 1.764 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1703 ; 1.085 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 119 ; 5.664 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 43 ;33.717 ;23.256 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 163 ;11.521 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.734 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 150 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1040 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 187 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 581 ; 0.975 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 949 ; 1.744 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 401 ; 2.846 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 372 ; 4.666 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 231 A 344 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0920 -13.4780 -4.6080 REMARK 3 T TENSOR REMARK 3 T11: 0.0047 T22: -0.0379 REMARK 3 T33: 0.0207 T12: -0.0137 REMARK 3 T13: 0.0339 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.7601 L22: 1.7168 REMARK 3 L33: 1.2982 L12: 0.1424 REMARK 3 L13: 0.2461 L23: 0.4109 REMARK 3 S TENSOR REMARK 3 S11: 0.0456 S12: -0.1177 S13: 0.0080 REMARK 3 S21: 0.2677 S22: -0.0903 S23: 0.0714 REMARK 3 S31: 0.0650 S32: -0.0680 S33: 0.0447 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2JLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1290037201. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22446 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 63.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2JLJ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 1 M SODIUM REMARK 280 MALONATE PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 33.33850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.93650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.93650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.00775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.93650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.93650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.66925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.93650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.93650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.00775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.93650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.93650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.66925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 33.33850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.6 KCAL/MOL 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.33850 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 263 TO ALA 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 ILE A 211 REMARK 465 LYS A 212 REMARK 465 GLU A 213 REMARK 465 LEU A 214 REMARK 465 LYS A 215 REMARK 465 MET A 216 REMARK 465 SER A 217 REMARK 465 LYS A 218 REMARK 465 ASP A 219 REMARK 465 GLU A 220 REMARK 465 ILE A 221 REMARK 465 LYS A 222 REMARK 465 ARG A 223 REMARK 465 GLU A 224 REMARK 465 TYR A 225 REMARK 465 LYS A 226 REMARK 465 GLU A 227 REMARK 465 MET A 228 REMARK 465 GLU A 229 REMARK 465 GLY A 230 REMARK 465 ASN A 345 REMARK 465 ILE A 346 REMARK 465 GLU A 347 REMARK 465 LYS A 348 REMARK 465 GLN A 349 REMARK 465 HIS A 350 REMARK 465 SER A 351 REMARK 465 GLU A 352 REMARK 465 MET A 353 REMARK 465 LEU A 354 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 LYS A 274 CG CD CE NZ REMARK 470 ARG A 275 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 277 CG CD OE1 OE2 REMARK 470 ARG A 296 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 342 CB CG CD OE1 OE2 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 HOH A 2047 O HOH A 2049 1.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG1 THR A 288 OH2 1PE A 1345 8554 2.11 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 319 CB - CG - OD1 ANGL. DEV. = 6.8 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 HIS A 266 -55.12 -127.32 REMARK 500 GLU A 277 -89.25 88.00 REMARK 500 ASP A 289 -130.04 55.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 1345 REMARK 610 1PE A 1346 REMARK 610 1PE A 1347 REMARK 610 1PE A 1348 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1348 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JLI RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF THE CYTOPLASMIC DOMAIN OF YERSINIA REMARK 900 PESTIS YSCU, A REGULATORY SWITCH INVOLVED IN TYPE III SECRETION REMARK 900 RELATED ID: 2JLJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF YERSINIA PESTIS YSCU REMARK 900 N263A P264A MUTANT DBREF 2JLH A 211 354 UNP P69986 YSCU_YERPE 211 354 SEQADV 2JLH ALA A 263 UNP P69986 ASN 263 ENGINEERED MUTATION SEQRES 1 A 144 ILE LYS GLU LEU LYS MET SER LYS ASP GLU ILE LYS ARG SEQRES 2 A 144 GLU TYR LYS GLU MET GLU GLY SER PRO GLU ILE LYS SER SEQRES 3 A 144 LYS ARG ARG GLN PHE HIS GLN GLU ILE GLN SER ARG ASN SEQRES 4 A 144 MET ARG GLU ASN VAL LYS ARG SER SER VAL VAL VAL ALA SEQRES 5 A 144 ALA PRO THR HIS ILE ALA ILE GLY ILE LEU TYR LYS ARG SEQRES 6 A 144 GLY GLU THR PRO LEU PRO LEU VAL THR PHE LYS TYR THR SEQRES 7 A 144 ASP ALA GLN VAL GLN THR VAL ARG LYS ILE ALA GLU GLU SEQRES 8 A 144 GLU GLY VAL PRO ILE LEU GLN ARG ILE PRO LEU ALA ARG SEQRES 9 A 144 ALA LEU TYR TRP ASP ALA LEU VAL ASP HIS TYR ILE PRO SEQRES 10 A 144 ALA GLU GLN ILE GLU ALA THR ALA GLU VAL LEU ARG TRP SEQRES 11 A 144 LEU GLU ARG GLN ASN ILE GLU LYS GLN HIS SER GLU MET SEQRES 12 A 144 LEU HET 1PE A1345 13 HET 1PE A1346 10 HET 1PE A1347 10 HET 1PE A1348 10 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 1PE 4(C10 H22 O6) FORMUL 6 HOH *129(H2 O) HELIX 1 1 SER A 231 GLN A 246 1 16 HELIX 2 2 ASN A 249 ARG A 256 1 8 HELIX 3 3 ALA A 290 GLY A 303 1 14 HELIX 4 4 ARG A 309 ALA A 320 1 12 HELIX 5 5 PRO A 327 GLU A 329 5 3 HELIX 6 6 GLN A 330 ARG A 343 1 14 SHEET 1 AA 4 LEU A 282 THR A 288 0 SHEET 2 AA 4 ILE A 267 LEU A 272 -1 O ALA A 268 N TYR A 287 SHEET 3 AA 4 VAL A 259 ALA A 263 -1 O VAL A 259 N ILE A 271 SHEET 4 AA 4 ILE A 306 GLN A 308 1 O LEU A 307 N ALA A 262 CISPEP 1 ARG A 275 GLY A 276 0 -0.98 CISPEP 2 GLY A 276 GLU A 277 0 -3.05 SITE 1 AC1 5 GLN A 243 THR A 288 ASP A 289 GLN A 291 SITE 2 AC1 5 TYR A 317 SITE 1 AC2 5 ARG A 248 ASN A 249 MET A 250 ARG A 251 SITE 2 AC2 5 TYR A 287 SITE 1 AC3 4 ILE A 306 LEU A 307 HOH A2060 HOH A2128 SITE 1 AC4 10 ARG A 309 ILE A 310 PRO A 311 LEU A 312 SITE 2 AC4 10 ALA A 315 GLN A 330 ALA A 333 HOH A2063 SITE 3 AC4 10 HOH A2102 HOH A2129 CRYST1 65.873 65.873 66.677 90.00 90.00 90.00 P 43 21 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 0.015181 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014998 0.00000