HEADER MEMBRANE PROTEIN 23-OCT-11 3UB6 TITLE PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH TITLE 2 UREA BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEMORECEPTOR TLPB; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PERIPLASMIC PORTION; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 102617; SOURCE 4 STRAIN: SS1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBH4 KEYWDS HOMODIMER, FOUR-HELIX BUNDLE, PAS DOMAIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.N.HENDERSON,E.G.SWEENEY,J.GOERS,C.WREDEN,K.G.HICKS,R.PARTHASARATHY, AUTHOR 2 K.J.GUILLEMIN,S.J.REMINGTON REVDAT 4 28-FEB-24 3UB6 1 REMARK DBREF REVDAT 3 08-NOV-17 3UB6 1 REMARK REVDAT 2 09-JAN-13 3UB6 1 JRNL REVDAT 1 27-JUN-12 3UB6 0 JRNL AUTH E.GOERS SWEENEY,J.N.HENDERSON,J.GOERS,C.WREDEN,K.G.HICKS, JRNL AUTH 2 J.K.FOSTER,R.PARTHASARATHY,S.J.REMINGTON,K.GUILLEMIN JRNL TITL STRUCTURE AND PROPOSED MECHANISM FOR THE PH-SENSING JRNL TITL 2 HELICOBACTER PYLORI CHEMORECEPTOR TLPB. JRNL REF STRUCTURE V. 20 1177 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22705207 JRNL DOI 10.1016/J.STR.2012.04.021 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 126197 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) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6320 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8688 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 419 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2550 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 575 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.15000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.841 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2838 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1930 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3852 ; 1.484 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4729 ; 0.909 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 379 ; 4.605 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;36.718 ;25.224 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 489 ; 9.654 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ; 6.576 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 401 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3208 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 581 ; 0.003 ; 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): 1702 ; 2.755 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 701 ; 1.515 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2749 ; 3.783 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1136 ; 5.962 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1076 ; 7.890 ; 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): 4768 ; 3.062 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 575 ;19.163 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4704 ; 8.378 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3UB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068534. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : ASYMMETRIC CUT SINGLE CRYSTAL REMARK 200 SI(220) REMARK 200 OPTICS : RH/PT COATED REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PIPES PH 6.5, 22% PEG 3350, 0.2 REMARK 280 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 39.80400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.26700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.94050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.26700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.80400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.94050 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 31 REMARK 465 SER A 32 REMARK 465 LYS A 33 REMARK 465 VAL A 34 REMARK 465 MET A 35 REMARK 465 GLN A 36 REMARK 465 LYS A 37 REMARK 465 ASP A 38 REMARK 465 VAL A 39 REMARK 465 PHE A 204 REMARK 465 ASN A 205 REMARK 465 GLU A 206 REMARK 465 ASN A 207 REMARK 465 THR A 208 REMARK 465 THR A 209 REMARK 465 ARG A 210 REMARK 465 LEU A 211 REMARK 465 GLY B 31 REMARK 465 SER B 32 REMARK 465 LYS B 33 REMARK 465 VAL B 34 REMARK 465 MET B 35 REMARK 465 GLN B 36 REMARK 465 LYS B 37 REMARK 465 ASP B 38 REMARK 465 VAL B 39 REMARK 465 PHE B 204 REMARK 465 ASN B 205 REMARK 465 GLU B 206 REMARK 465 ASN B 207 REMARK 465 THR B 208 REMARK 465 THR B 209 REMARK 465 ARG B 210 REMARK 465 LEU B 211 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 40 CG CD1 CD2 REMARK 470 ALA A 41 CB REMARK 470 GLN A 42 CG CD OE1 NE2 REMARK 470 LEU A 43 CD1 CD2 REMARK 470 MET A 44 CE REMARK 470 GLU A 45 CD OE1 OE2 REMARK 470 HIS A 46 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 84 CD CE NZ REMARK 470 LYS A 97 NZ REMARK 470 LYS A 107 CE NZ REMARK 470 LYS A 119 NZ REMARK 470 LYS A 145 CE NZ REMARK 470 LYS A 146 CE NZ REMARK 470 LYS A 165 NZ REMARK 470 LYS A 194 CD CE NZ REMARK 470 LYS A 197 CE NZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 VAL A 203 CG1 CG2 REMARK 470 LEU B 40 CD1 CD2 REMARK 470 ALA B 41 CB REMARK 470 GLN B 42 CG CD OE1 NE2 REMARK 470 MET B 44 CE REMARK 470 GLU B 45 CD OE1 OE2 REMARK 470 HIS B 46 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 53 CD CE NZ REMARK 470 LYS B 57 CE NZ REMARK 470 LYS B 97 CE NZ REMARK 470 LYS B 119 NZ REMARK 470 LYS B 145 CD CE NZ REMARK 470 LYS B 146 CE NZ REMARK 470 LYS B 194 CE NZ REMARK 470 LYS B 197 CE NZ REMARK 470 LYS B 202 CB CG CD CE NZ REMARK 470 VAL B 203 CG1 CG2 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 ARG A 83 CG ARG A 83 CD -0.212 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 ARG A 83 NE - CZ - NH1 ANGL. DEV. = -3.9 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 ASP A 114 86.71 -168.08 REMARK 500 ASP B 114 88.06 -168.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 78 0.10 SIDE CHAIN REMARK 500 PHE B 77 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URE B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UB7 RELATED DB: PDB REMARK 900 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB REMARK 900 WITH ACETAMIDE BOUND REMARK 900 RELATED ID: 3UB8 RELATED DB: PDB REMARK 900 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB REMARK 900 WITH FORMAMIDE BOUND REMARK 900 RELATED ID: 3UB9 RELATED DB: PDB REMARK 900 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB REMARK 900 WITH HYDROXYUREA BOUND DBREF 3UB6 A 31 211 PDB 3UB6 3UB6 31 211 DBREF 3UB6 B 31 211 PDB 3UB6 3UB6 31 211 SEQRES 1 A 181 GLY SER LYS VAL MET GLN LYS ASP VAL LEU ALA GLN LEU SEQRES 2 A 181 MET GLU HIS LEU GLU THR GLY GLN TYR LYS LYS ARG GLU SEQRES 3 A 181 LYS THR LEU ALA TYR MET THR LYS ILE LEU GLU GLN GLY SEQRES 4 A 181 ILE HIS GLU TYR TYR LYS SER PHE ASP ASN ASP THR ALA SEQRES 5 A 181 ARG LYS MET ALA LEU ASP TYR PHE LYS ARG ILE ASN ASP SEQRES 6 A 181 ASP LYS GLY MET ILE TYR MET VAL VAL VAL ASP LYS ASN SEQRES 7 A 181 GLY VAL VAL LEU PHE ASP PRO VAL ASN PRO LYS THR VAL SEQRES 8 A 181 GLY GLN SER GLY LEU ASP ALA GLN SER VAL ASP GLY VAL SEQRES 9 A 181 TYR TYR VAL ARG GLY TYR LEU GLU ALA ALA LYS LYS GLY SEQRES 10 A 181 GLY GLY TYR THR TYR TYR LYS MET PRO LYS TYR ASP GLY SEQRES 11 A 181 GLY VAL PRO GLU LYS LYS PHE ALA TYR SER HIS TYR ASP SEQRES 12 A 181 GLU VAL SER GLN MET VAL ILE ALA ALA THR SER TYR TYR SEQRES 13 A 181 THR ASP ILE ASN THR GLU ASN LYS ALA ILE LYS GLU GLY SEQRES 14 A 181 VAL ASN LYS VAL PHE ASN GLU ASN THR THR ARG LEU SEQRES 1 B 181 GLY SER LYS VAL MET GLN LYS ASP VAL LEU ALA GLN LEU SEQRES 2 B 181 MET GLU HIS LEU GLU THR GLY GLN TYR LYS LYS ARG GLU SEQRES 3 B 181 LYS THR LEU ALA TYR MET THR LYS ILE LEU GLU GLN GLY SEQRES 4 B 181 ILE HIS GLU TYR TYR LYS SER PHE ASP ASN ASP THR ALA SEQRES 5 B 181 ARG LYS MET ALA LEU ASP TYR PHE LYS ARG ILE ASN ASP SEQRES 6 B 181 ASP LYS GLY MET ILE TYR MET VAL VAL VAL ASP LYS ASN SEQRES 7 B 181 GLY VAL VAL LEU PHE ASP PRO VAL ASN PRO LYS THR VAL SEQRES 8 B 181 GLY GLN SER GLY LEU ASP ALA GLN SER VAL ASP GLY VAL SEQRES 9 B 181 TYR TYR VAL ARG GLY TYR LEU GLU ALA ALA LYS LYS GLY SEQRES 10 B 181 GLY GLY TYR THR TYR TYR LYS MET PRO LYS TYR ASP GLY SEQRES 11 B 181 GLY VAL PRO GLU LYS LYS PHE ALA TYR SER HIS TYR ASP SEQRES 12 B 181 GLU VAL SER GLN MET VAL ILE ALA ALA THR SER TYR TYR SEQRES 13 B 181 THR ASP ILE ASN THR GLU ASN LYS ALA ILE LYS GLU GLY SEQRES 14 B 181 VAL ASN LYS VAL PHE ASN GLU ASN THR THR ARG LEU HET URE A 301 4 HET SO4 A 302 5 HET PEG A 303 7 HET SO4 A 304 5 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET URE B 301 4 HET SO4 B 302 5 HET GOL B 303 6 HET GOL B 304 6 HET GOL B 305 6 HET GOL B 306 6 HET GOL B 307 6 HETNAM URE UREA HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 URE 2(C H4 N2 O) FORMUL 4 SO4 3(O4 S 2-) FORMUL 5 PEG C4 H10 O3 FORMUL 7 GOL 9(C3 H8 O3) FORMUL 18 HOH *575(H2 O) HELIX 1 1 LEU A 40 PHE A 77 1 38 HELIX 2 2 ASP A 78 ASP A 96 1 19 HELIX 3 3 ASN A 117 VAL A 121 5 5 HELIX 4 4 TYR A 135 LYS A 146 1 12 HELIX 5 5 TYR A 186 ASN A 193 1 8 HELIX 6 6 ASN A 193 VAL A 203 1 11 HELIX 7 7 ALA B 41 LYS B 75 1 35 HELIX 8 8 ASP B 78 LYS B 97 1 20 HELIX 9 9 ASN B 117 VAL B 121 5 5 HELIX 10 10 TYR B 135 LYS B 146 1 12 HELIX 11 11 TYR B 186 ASN B 193 1 8 HELIX 12 12 ASN B 193 VAL B 203 1 11 SHEET 1 A 5 VAL A 111 PHE A 113 0 SHEET 2 A 5 TYR A 101 VAL A 105 -1 N VAL A 104 O LEU A 112 SHEET 3 A 5 MET A 178 TYR A 185 -1 O VAL A 179 N VAL A 105 SHEET 4 A 5 GLU A 164 ASP A 173 -1 N ASP A 173 O MET A 178 SHEET 5 A 5 GLY A 149 MET A 155 -1 N GLY A 149 O SER A 170 SHEET 1 B 5 VAL B 111 PHE B 113 0 SHEET 2 B 5 TYR B 101 ASP B 106 -1 N VAL B 104 O LEU B 112 SHEET 3 B 5 MET B 178 TYR B 185 -1 O VAL B 179 N VAL B 105 SHEET 4 B 5 GLU B 164 ASP B 173 -1 N ASP B 173 O MET B 178 SHEET 5 B 5 GLY B 149 MET B 155 -1 N TYR B 153 O LYS B 166 SITE 1 AC1 7 VAL A 103 ASP A 114 TYR A 136 TYR A 140 SITE 2 AC1 7 TYR A 153 LYS A 166 HOH A 407 SITE 1 AC2 9 LYS A 54 ARG A 55 THR A 58 MET A 99 SITE 2 AC2 9 HOH A 450 LYS B 54 SO4 B 302 HOH B 641 SITE 3 AC2 9 HOH B 669 SITE 1 AC3 5 GLN A 68 HIS A 71 HOH A 667 HOH A 679 SITE 2 AC3 5 ARG B 92 SITE 1 AC4 5 GLN A 68 HIS A 71 HOH A 417 HOH A 667 SITE 2 AC4 5 ARG B 92 SITE 1 AC5 6 GLY A 98 MET A 99 GLU A 192 HOH A 511 SITE 2 AC5 6 HOH A 593 HOH A 613 SITE 1 AC6 3 TYR A 52 TYR A 186 HOH A 493 SITE 1 AC7 3 LYS A 119 GLN A 123 ASN B 108 SITE 1 AC8 6 VAL A 134 TYR A 135 HOH A 488 HOH A 616 SITE 2 AC8 6 HOH A 638 HOH A 652 SITE 1 AC9 7 VAL B 103 ASP B 114 TYR B 136 TYR B 140 SITE 2 AC9 7 TYR B 153 LYS B 166 HOH B 403 SITE 1 BC1 8 LYS A 54 SO4 A 302 LYS B 54 ARG B 55 SITE 2 BC1 8 THR B 58 HOH B 439 HOH B 641 HOH B 669 SITE 1 BC2 12 ASN B 94 ASP B 95 LYS B 157 GOL B 307 SITE 2 BC2 12 HOH B 411 HOH B 430 HOH B 438 HOH B 486 SITE 3 BC2 12 HOH B 498 HOH B 523 HOH B 539 HOH B 602 SITE 1 BC3 8 LYS B 97 GLY B 98 MET B 99 GLU B 192 SITE 2 BC3 8 HOH B 409 HOH B 517 HOH B 651 HOH B 658 SITE 1 BC4 3 TYR B 52 LYS B 165 HOH B 613 SITE 1 BC5 3 TYR B 158 HOH B 429 HOH B 676 SITE 1 BC6 5 TYR B 158 GOL B 303 HOH B 438 HOH B 523 SITE 2 BC6 5 HOH B 602 CRYST1 79.608 81.881 94.534 90.00 90.00 90.00 P 21 21 21 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 0.012562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010578 0.00000