HEADER NUCLEOTIDE-BINDING PROTEIN 26-FEB-97 5RHN
TITLE HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT
TITLE 2 COMPLEXED WITH 8-BR-AMP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: HINT;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS;
SOURCE 3 ORGANISM_COMMON: RABBIT;
SOURCE 4 ORGANISM_TAXID: 9986;
SOURCE 5 ORGAN: HEART;
SOURCE 6 GENE: HINT;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: JM109/DE3/LACIQ;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: LAC;
SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PSGA02;
SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PSGA02-HINT;
SOURCE 13 EXPRESSION_SYSTEM_GENE: HINT;
SOURCE 14 OTHER_DETAILS: RABBIT HINT CDNA WAS CLONED FROM HEART LIBRARY,
SOURCE 15 EXPRESSED IN ESCHERICHIA COLI, AND PURIFIED BY ADENOSINE-AGAROSE
SOURCE 16 AFFINITY CHROMATOGRAPHY
KEYWDS NUCLEOTIDE-BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.BRENNER,P.GARRISON,J.GILMOUR,D.PEISACH,D.RINGE,G.A.PETSKO,
AUTHOR 2 J.M.LOWENSTEIN
REVDAT 4 06-MAR-24 5RHN 1 REMARK
REVDAT 3 13-JUL-11 5RHN 1 VERSN
REVDAT 2 24-FEB-09 5RHN 1 VERSN
REVDAT 1 16-JUN-97 5RHN 0
JRNL AUTH C.BRENNER,P.GARRISON,J.GILMOUR,D.PEISACH,D.RINGE,G.A.PETSKO,
JRNL AUTH 2 J.M.LOWENSTEIN
JRNL TITL CRYSTAL STRUCTURES OF HINT DEMONSTRATE THAT HISTIDINE TRIAD
JRNL TITL 2 PROTEINS ARE GALT-RELATED NUCLEOTIDE-BINDING PROTEINS.
JRNL REF NAT.STRUCT.BIOL. V. 4 231 1997
JRNL REFN ISSN 1072-8368
JRNL PMID 9164465
JRNL DOI 10.1038/NSB0397-231
REMARK 2
REMARK 2 RESOLUTION. 2.31 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) : 2.31
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 5478
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.162
REMARK 3 FREE R VALUE : 0.264
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000
REMARK 3 FREE R VALUE TEST SET COUNT : 471
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 8
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.31
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 559
REMARK 3 BIN R VALUE (WORKING SET) : 0.1970
REMARK 3 BIN FREE R VALUE : 0.2830
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.80
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 54
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 878
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 24
REMARK 3 SOLVENT ATOMS : 51
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) : 0.011
REMARK 3 BOND ANGLES (DEGREES) : 1.710
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460
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 : PARHCSDX.PRO
REMARK 3 PARAMETER FILE 2 : RIB.PAR
REMARK 3 PARAMETER FILE 3 : WATER.PARAM
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO
REMARK 3 TOPOLOGY FILE 2 : WATER.TOPH
REMARK 3 TOPOLOGY FILE 3 : RIB.TOP
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5RHN 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_1000179766.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : JUL-96
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NI FILTER
REMARK 200 OPTICS : COLLIMATOR
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200 DATA SCALING SOFTWARE : R-AXIS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5578
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310
REMARK 200 RESOLUTION RANGE LOW (A) : 35.130
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 8.200
REMARK 200 R MERGE (I) : 0.08400
REMARK 200 R SYM (I) : 0.05000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3
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 <I/SIGMA(I)> 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: 5RHN (TETRAGONAL HINT-8-BR-AMP, ISOMORPHOUS WITH HINT
REMARK 200 WITHOUT NUCLEOTIDE) WAS DETERMINED BY REFINEMENT OF HINT WITHOUT
REMARK 200 NUCLEOTIDE.
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% POLYETHYLENE GLYCOL 8000, 0.1 M
REMARK 280 SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5
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 71.54000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.16000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.16000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.31000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.16000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.16000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.77000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.16000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.16000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 107.31000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.16000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.16000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.77000
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 71.54000
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: PISA,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 5170 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 143.08000
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 ARG A 12 CG CD NE CZ NH1 NH2
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 16 68.91 -116.07
REMARK 500 TYR A 94 -179.23 -171.77
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: HIT
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: THE HISTIDINE TRIAD FORMS PART OF THE ALPHA
REMARK 800 PHOSPHATE-BINDING LOOP IN THE HIT PROTEIN SUPERFAMILY OF
REMARK 800 NUCLEOTIDE-BINDING PROTEINS.
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 8BR A 201
DBREF 5RHN A 12 126 UNP P80912 HINT1_RABIT 11 125
SEQRES 1 A 115 ARG PRO GLY GLY ASP THR ILE PHE GLY LYS ILE ILE ARG
SEQRES 2 A 115 LYS GLU ILE PRO ALA LYS ILE ILE PHE GLU ASP ASP GLN
SEQRES 3 A 115 CYS LEU ALA PHE HIS ASP ILE SER PRO GLN ALA PRO THR
SEQRES 4 A 115 HIS PHE LEU VAL ILE PRO LYS LYS HIS ILE SER GLN ILE
SEQRES 5 A 115 SER ALA ALA GLU ASP ALA ASP GLU SER LEU LEU GLY HIS
SEQRES 6 A 115 LEU MET ILE VAL GLY LYS LYS CYS ALA ALA ASP LEU GLY
SEQRES 7 A 115 LEU LYS LYS GLY TYR ARG MET VAL VAL ASN GLU GLY SER
SEQRES 8 A 115 ASP GLY GLY GLN SER VAL TYR HIS VAL HIS LEU HIS VAL
SEQRES 9 A 115 LEU GLY GLY ARG GLN MET ASN TRP PRO PRO GLY
HET 8BR A 201 24
HETNAM 8BR 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE
FORMUL 2 8BR C10 H13 BR N5 O7 P
FORMUL 3 HOH *51(H2 O)
HELIX 1 A1 THR A 17 LYS A 25 1 9
HELIX 2 A2 ASP A 68 GLY A 89 1 22
SHEET 1 B 5 TYR A 94 VAL A 97 0
SHEET 2 B 5 HIS A 112 GLY A 117 -1 N LEU A 116 O ARG A 95
SHEET 3 B 5 THR A 50 PRO A 56 -1 N VAL A 54 O LEU A 113
SHEET 4 B 5 CYS A 38 HIS A 42 -1 N PHE A 41 O LEU A 53
SHEET 5 B 5 ILE A 31 GLU A 34 -1 N PHE A 33 O ALA A 40
CISPEP 1 TRP A 123 PRO A 124 0 0.31
SITE 1 HIT 3 HIS A 110 HIS A 112 HIS A 114
SITE 1 AC1 17 PHE A 19 LYS A 25 GLU A 34 PHE A 41
SITE 2 AC1 17 HIS A 42 ASP A 43 ILE A 44 SER A 45
SITE 3 AC1 17 ASN A 99 GLY A 105 GLN A 106 SER A 107
SITE 4 AC1 17 VAL A 108 HIS A 112 HIS A 114 HOH A 251
SITE 5 AC1 17 HOH A 261
CRYST1 40.320 40.320 143.080 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 0.024802 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024802 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006989 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
