HEADER SIGNALING PROTEIN 04-JUN-01 1JBE TITLE 1.08 A STRUCTURE OF APO-CHEY REVEALS META-ACTIVE CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEMOTAXIS PROTEIN CHEY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHEY, CHEMOTAXIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SIMONOVIC,K.VOLZ REVDAT 11 20-NOV-24 1JBE 1 REMARK REVDAT 10 07-FEB-24 1JBE 1 COMPND SEQADV SEQRES HET REVDAT 10 2 1 HETNAM HETSYN FORMUL LINK REVDAT 10 3 1 SITE ATOM REVDAT 9 15-NOV-23 1JBE 1 LINK ATOM REVDAT 8 16-AUG-23 1JBE 1 REMARK LINK REVDAT 7 18-SEP-19 1JBE 1 COMPND SOURCE DBREF SEQADV REVDAT 6 24-JUL-19 1JBE 1 REMARK LINK REVDAT 5 13-JUL-11 1JBE 1 VERSN REVDAT 4 24-FEB-09 1JBE 1 VERSN REVDAT 3 01-APR-03 1JBE 1 JRNL REVDAT 2 09-OCT-02 1JBE 1 REMARK REVDAT 1 08-AUG-01 1JBE 0 JRNL AUTH M.SIMONOVIC,K.VOLZ JRNL TITL A DISTINCT META-ACTIVE CONFORMATION IN THE 1.1-A RESOLUTION JRNL TITL 2 STRUCTURE OF WILD-TYPE APOCHEY. JRNL REF J.BIOL.CHEM. V. 276 28637 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11410584 JRNL DOI 10.1074/JBC.C100295200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SIMONOVIC,K.VOLZ REMARK 1 TITL ATOMIC RESOLUTION STRUCTURE OF A SUCCINIMIDE INTERMEDIATE IN REMARK 1 TITL 2 E. COLI CHEY REMARK 1 REF J.MOL.BIOL. V. 322 663 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1016/S0022-2836(02)00821-5 REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.113 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4210 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 42133 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.106 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.114 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3757 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 37598 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 978 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1216.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1996.1 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 14 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 16023 REMARK 3 NUMBER OF RESTRAINTS : 15497 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.022 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.016 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.044 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.065 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.002 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.041 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.087 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1JBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.08 REMARK 200 R MERGE FOR SHELL (I) : 0.21200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: APO-CHEY (PDB CODE: 3CHY) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICRODIALYSIS, 2.2M AMMONIUM SULFATE, REMARK 280 50MM TRIS, PH 8.3, MICRODIALYSIS, TEMPERATURE 293K 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 22.56100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.56000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.32600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.56000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.56100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.32600 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 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 19 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 106 CA - CB - CG ANGL. DEV. = 13.0 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 ASN A 62 -58.47 75.08 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 SO4 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 SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CHY RELATED DB: PDB REMARK 900 3CHY IS THE 1.7 A STRUCTURE OF APO-CHEY DBREF 1JBE A 2 129 UNP P0AE67 CHEY_ECOLI 2 129 SEQADV 1JBE SNN A 75 UNP P0AE67 ASP 75 MODIFIED RESIDUE SEQRES 1 A 128 ALA ASP LYS GLU LEU LYS PHE LEU VAL VAL ASP ASP PHE SEQRES 2 A 128 SER THR MET ARG ARG ILE VAL ARG ASN LEU LEU LYS GLU SEQRES 3 A 128 LEU GLY PHE ASN ASN VAL GLU GLU ALA GLU ASP GLY VAL SEQRES 4 A 128 ASP ALA LEU ASN LYS LEU GLN ALA GLY GLY TYR GLY PHE SEQRES 5 A 128 VAL ILE SER ASP TRP ASN MET PRO ASN MET ASP GLY LEU SEQRES 6 A 128 GLU LEU LEU LYS THR ILE ARG ALA SNN GLY ALA MET SER SEQRES 7 A 128 ALA LEU PRO VAL LEU MET VAL THR ALA GLU ALA LYS LYS SEQRES 8 A 128 GLU ASN ILE ILE ALA ALA ALA GLN ALA GLY ALA SER GLY SEQRES 9 A 128 TYR VAL VAL LYS PRO PHE THR ALA ALA THR LEU GLU GLU SEQRES 10 A 128 LYS LEU ASN LYS ILE PHE GLU LYS LEU GLY MET MODRES 1JBE SNN A 75 ASN L-3-AMINOSUCCINIMIDE HET SNN A 75 8 HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET GOL A 201 6 HET GOL A 202 6 HETNAM SNN L-3-AMINOSUCCINIMIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SNN C4 H6 N2 O2 FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *198(H2 O) HELIX 1 1 PHE A 14 LEU A 28 1 15 HELIX 2 2 ASP A 38 GLN A 47 1 10 HELIX 3 3 ASP A 64 ALA A 74 1 11 HELIX 4 4 LYS A 91 ALA A 101 1 11 HELIX 5 5 THR A 112 GLY A 128 1 17 SHEET 1 A 5 VAL A 33 ALA A 36 0 SHEET 2 A 5 PHE A 8 VAL A 11 1 O PHE A 8 N GLU A 34 SHEET 3 A 5 PHE A 53 ASP A 57 1 O PHE A 53 N LEU A 9 SHEET 4 A 5 VAL A 83 THR A 87 1 N LEU A 84 O VAL A 54 SHEET 5 A 5 GLY A 105 VAL A 108 1 O GLY A 105 N MET A 85 LINK C ALA A 74 N SNN A 75 1555 1555 1.32 LINK N1 SNN A 75 CA GLY A 76 1555 1555 1.44 LINK C GLY A 76 N ALA A 77 1555 1555 1.32 CISPEP 1 LYS A 109 PRO A 110 0 -5.59 SITE 1 AC1 6 ASN A 59 LYS A 109 GOL A 201 HOH A 411 SITE 2 AC1 6 HOH A 416 HOH A 460 SITE 1 AC2 11 PRO A 61 ASN A 62 GLY A 105 TYR A 106 SITE 2 AC2 11 LYS A 119 LYS A 122 HOH A 424 HOH A 428 SITE 3 AC2 11 HOH A 441 HOH A 448 HOH A 451 SITE 1 AC3 12 ASP A 13 PHE A 14 SER A 15 ALA A 74 SITE 2 AC3 12 SNN A 75 GLY A 76 GLN A 100 GOL A 202 SITE 3 AC3 12 HOH A 410 HOH A 528 HOH A 549 HOH A 551 SITE 1 AC4 9 ASP A 12 PHE A 14 MET A 17 GLN A 47 SITE 2 AC4 9 LYS A 109 SO4 A 301 HOH A 457 HOH A 460 SITE 3 AC4 9 HOH A 537 SITE 1 AC5 6 ASP A 13 SER A 15 ARG A 18 GLU A 37 SITE 2 AC5 6 SO4 A 303 HOH A 414 CRYST1 45.122 46.652 53.120 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 0.022162 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018825 0.00000