HEADER MEMBRANE PROTEIN 23-OCT-11 3UB8 TITLE PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH TITLE 2 FORMAMIDE 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 3 08-NOV-17 3UB8 1 REMARK REVDAT 2 09-JAN-13 3UB8 1 JRNL REVDAT 1 27-JUN-12 3UB8 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. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.8 REMARK 3 NUMBER OF REFLECTIONS : 92865 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4683 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) : 1.42 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6702 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 353 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 428 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.27000 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): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.044 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2631 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1755 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3549 ; 1.492 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4293 ; 0.921 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 333 ; 5.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;36.329 ;24.918 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 454 ;10.684 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 6.132 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2940 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 532 ; 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): 1601 ; 2.772 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 667 ; 1.463 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2560 ; 3.662 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1030 ; 5.678 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 980 ; 7.629 ; 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): 4386 ; 2.904 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 428 ;17.359 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4336 ; 8.026 ; 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 3UB8 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_1000068536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-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 : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : RH/PT COATED SI REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92912 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 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 (%) : 79.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 2.1 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 39.80500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.26900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.85650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.26900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.80500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.85650 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: 5240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 LEU A 40 REMARK 465 ALA A 41 REMARK 465 GLN A 42 REMARK 465 LEU A 43 REMARK 465 ASN A 201 REMARK 465 LYS A 202 REMARK 465 VAL A 203 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 LEU B 40 REMARK 465 ALA B 41 REMARK 465 GLN B 42 REMARK 465 LEU B 43 REMARK 465 LYS B 202 REMARK 465 VAL B 203 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 MET A 44 CG SD CE REMARK 470 GLU A 45 CG CD OE1 OE2 REMARK 470 HIS A 46 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 84 NZ REMARK 470 LYS A 107 CE NZ REMARK 470 LYS A 119 CE NZ REMARK 470 LYS A 145 CE NZ REMARK 470 LYS A 194 CE NZ REMARK 470 LYS A 197 CG CD CE NZ REMARK 470 GLU A 198 CG CD OE1 OE2 REMARK 470 GLU B 45 CB CG CD OE1 OE2 REMARK 470 HIS B 46 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 75 CD CE NZ REMARK 470 LYS B 119 NZ REMARK 470 LYS B 145 CD CE NZ REMARK 470 LYS B 194 CE NZ REMARK 470 LYS B 197 CE NZ 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 -0.161 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 B 78 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG B 92 NE - CZ - NH1 ANGL. DEV. = -3.6 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 89.29 -168.27 REMARK 500 ASP B 114 87.95 -166.01 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 0.07 SIDE CHAIN REMARK 500 ASP B 78 0.11 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 ARF 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 ARF A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARF A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARF A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARF 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 SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARF B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARF B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARF B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UB6 RELATED DB: PDB REMARK 900 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB REMARK 900 WITH UREA BOUND 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: 3UB9 RELATED DB: PDB REMARK 900 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB REMARK 900 WITH HYDROXYUREA BOUND DBREF 3UB8 A 31 211 PDB 3UB8 3UB8 1 181 DBREF 3UB8 B 31 211 PDB 3UB8 3UB8 1 181 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 ARF A 301 3 HET SO4 A 302 5 HET ARF A 303 3 HET ARF A 304 3 HET ARF A 305 3 HET ARF A 306 3 HET GOL A 307 6 HET ARF B 302 3 HET SO4 B 301 5 HET ARF B 303 3 HET ARF B 304 3 HET GOL B 305 6 HETNAM ARF FORMAMIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ARF 8(C H3 N O) FORMUL 4 SO4 2(O4 S 2-) FORMUL 9 GOL 2(C3 H8 O3) FORMUL 15 HOH *428(H2 O) HELIX 1 1 MET A 44 PHE A 77 1 34 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 200 1 8 HELIX 7 7 GLU B 45 LYS B 75 1 31 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 ASN B 201 1 9 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 TYR A 169 O ALA A 182 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 TYR B 169 O ALA B 182 SHEET 5 B 5 GLY B 149 MET B 155 -1 N MET B 155 O GLU B 164 SITE 1 AC1 5 LYS A 54 SO4 A 302 HOH A 535 ARG B 55 SITE 2 AC1 5 THR B 58 SITE 1 AC2 8 LYS A 54 ARG A 55 THR A 58 MET A 99 SITE 2 AC2 8 ARF A 301 HOH A 463 LYS B 54 SO4 B 301 SITE 1 AC3 7 VAL A 103 ASP A 114 VAL A 116 TYR A 153 SITE 2 AC3 7 MET A 155 LYS A 166 HOH A 406 SITE 1 AC4 6 VAL A 103 ASP A 114 TYR A 136 TYR A 140 SITE 2 AC4 6 TYR A 153 LYS A 166 SITE 1 AC5 5 VAL A 103 ASP A 114 TYR A 136 TYR A 140 SITE 2 AC5 5 HOH A 406 SITE 1 AC6 5 ARG A 55 THR A 58 HOH A 463 LYS B 54 SITE 2 AC6 5 SO4 B 301 SITE 1 AC7 6 LYS A 97 GLY A 98 MET A 99 ASP A 188 SITE 2 AC7 6 GLU A 192 HOH A 448 SITE 1 AC8 8 LYS A 54 SO4 A 302 ARF A 306 HOH A 535 SITE 2 AC8 8 LYS B 54 ARG B 55 THR B 58 MET B 99 SITE 1 AC9 7 VAL B 103 ASP B 114 TYR B 136 TYR B 140 SITE 2 AC9 7 TYR B 153 MET B 155 LYS B 166 SITE 1 BC1 7 VAL B 103 ASP B 114 VAL B 116 TYR B 153 SITE 2 BC1 7 MET B 155 LYS B 166 HOH B 407 SITE 1 BC2 6 VAL B 103 ASP B 114 VAL B 116 ASN B 117 SITE 2 BC2 6 TYR B 136 TYR B 140 SITE 1 BC3 12 ASN B 94 ASP B 95 LYS B 157 TYR B 158 SITE 2 BC3 12 HOH B 408 HOH B 411 HOH B 415 HOH B 455 SITE 3 BC3 12 HOH B 468 HOH B 469 HOH B 619 HOH B 621 CRYST1 79.610 81.713 94.538 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 0.012561 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010578 0.00000 MASTER 451 0 12 12 10 0 25 6 0 0 0 28 END