HEADER HISTIDINE-BINDING PROTEIN 30-SEP-93 1HPB TITLE THE BACTERIAL PERIPLASMIC HISTIDINE-BINDING PROTEIN: STRUCTURE(SLASH) TITLE 2 FUNCTION ANALYSIS OF THE LIGAND-BINDING SITE AND COMPARISON WITH TITLE 3 RELATED PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE-BINDING PROTEIN; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM; SOURCE 3 ORGANISM_TAXID: 602 KEYWDS HISTIDINE-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN P AUTHOR S.H.KIM,B.H.OH REVDAT 4 07-FEB-24 1HPB 1 REMARK REVDAT 3 29-NOV-17 1HPB 1 HELIX REVDAT 2 24-FEB-09 1HPB 1 VERSN REVDAT 1 26-JAN-95 1HPB 0 JRNL AUTH B.H.OH,C.H.KANG,H.DE BONDT,S.H.KIM,K.NIKAIDO,A.K.JOSHI, JRNL AUTH 2 G.F.AMES JRNL TITL THE BACTERIAL PERIPLASMIC HISTIDINE-BINDING PROTEIN. JRNL TITL 2 STRUCTURE/FUNCTION ANALYSIS OF THE LIGAND-BINDING SITE AND JRNL TITL 3 COMPARISON WITH RELATED PROTEINS. JRNL REF J.BIOL.CHEM. V. 269 4135 1994 JRNL REFN ISSN 0021-9258 JRNL PMID 8307974 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.-H.OH,J.PANDIT,C.-H.KANG,K.NIKAIDO,S.GOKCEN,G.F.AMES, REMARK 1 AUTH 2 S.-H.KIM REMARK 1 TITL THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, REMARK 1 TITL 2 ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A REMARK 1 TITL 3 LIGAND REMARK 1 REF J.BIOL.CHEM. V. 268 11348 1993 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.-H.KANG,W.-C.SHIN,Y.YAMAGATA,S.GOKCEN,G.F.-L.AMES,S.-H.KIM REMARK 1 TITL CRYSTAL STRUCTURE OF THE LYSINE-, ARGININE-, REMARK 1 TITL 2 ORNITHINE-BINDING PROTEIN FROM SALMONELLA TYPHIMURIUM AT 2.7 REMARK 1 TITL 3 ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 266 23893 1992 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.192 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 3.640 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 19.63000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.06500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.06500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.63000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.08500 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: P 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HIS P 240 DBREF 1HPB P 1 238 UNP P02910 HISJ_SALTY 23 260 SEQRES 1 P 238 ALA ILE PRO GLN LYS ILE ARG ILE GLY THR ASP PRO THR SEQRES 2 P 238 TYR ALA PRO PHE GLU SER LYS ASN ALA GLN GLY GLU LEU SEQRES 3 P 238 VAL GLY PHE ASP ILE ASP LEU ALA LYS GLU LEU CYS LYS SEQRES 4 P 238 ARG ILE ASN THR GLN CYS THR PHE VAL GLU ASN PRO LEU SEQRES 5 P 238 ASP ALA LEU ILE PRO SER LEU LYS ALA LYS LYS ILE ASP SEQRES 6 P 238 ALA ILE MET SER SER LEU SER ILE THR GLU LYS ARG GLN SEQRES 7 P 238 GLN GLU ILE ALA PHE THR ASP LYS LEU TYR ALA ALA ASP SEQRES 8 P 238 SER ARG LEU VAL VAL ALA LYS ASN SER ASP ILE GLN PRO SEQRES 9 P 238 THR VAL ALA SER LEU LYS GLY LYS ARG VAL GLY VAL LEU SEQRES 10 P 238 GLN GLY THR THR GLN GLU THR PHE GLY ASN GLU HIS TRP SEQRES 11 P 238 ALA PRO LYS GLY ILE GLU ILE VAL SER TYR GLN GLY GLN SEQRES 12 P 238 ASP ASN ILE TYR SER ASP LEU THR ALA GLY ARG ILE ASP SEQRES 13 P 238 ALA ALA PHE GLN ASP GLU VAL ALA ALA SER GLU GLY PHE SEQRES 14 P 238 LEU LYS GLN PRO VAL GLY LYS ASP TYR LYS PHE GLY GLY SEQRES 15 P 238 PRO ALA VAL LYS ASP GLU LYS LEU PHE GLY VAL GLY THR SEQRES 16 P 238 GLY MET GLY LEU ARG LYS GLU ASP ASN GLU LEU ARG GLU SEQRES 17 P 238 ALA LEU ASN LYS ALA PHE ALA GLU MET ARG ALA ASP GLY SEQRES 18 P 238 THR TYR GLU LYS LEU ALA LYS LYS TYR PHE ASP PHE ASP SEQRES 19 P 238 VAL TYR GLY GLY HET HIS P 240 11 HETNAM HIS HISTIDINE FORMUL 2 HIS C6 H10 N3 O2 1+ HELIX 1 A PHE P 29 ARG P 40 1 12 HELIX 2 B LEU P 52 LYS P 60 1 9 HELIX 3 C GLU P 75 GLU P 80 1 6 HELIX 4 D VAL P 106 LEU P 109 1 4 HELIX 5 E THR P 121 HIS P 129 1 9 HELIX 6 F GLN P 143 THR P 151 1 9 HELIX 7 G GLU P 162 GLY P 168 1 7 HELIX 8 H ASN P 204 ALA P 219 1 16 HELIX 9 I THR P 222 TYR P 230 1 9 SHEET 1 S1 5 GLN P 44 GLU P 49 0 SHEET 2 S1 5 LYS P 5 THR P 10 1 SHEET 3 S1 5 ALA P 66 SER P 72 1 SHEET 4 S1 5 MET P 197 LEU P 199 -1 SHEET 5 S1 5 ALA P 82 PHE P 83 -1 SHEET 1 S2 5 GLU P 136 TYR P 140 0 SHEET 2 S2 5 ARG P 113 LEU P 117 1 SHEET 3 S2 5 ALA P 157 ASP P 161 1 SHEET 4 S2 5 SER P 92 ALA P 97 -1 SHEET 5 S2 5 TYR P 178 PHE P 180 1 SITE 1 AC1 2 LEU P 71 THR P 120 CRYST1 39.260 66.170 88.130 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 0.025471 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011347 0.00000