PDB Short entry for 3RHN HEADER NUCLEOTIDE-BINDING PROTEIN 11-FEB-97 3RHN TITLE HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT TITLE 2 COMPLEXED WITH GMP 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 HISTIDINE, 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 21-FEB-24 3RHN 1 REMARK REVDAT 3 13-JUL-11 3RHN 1 VERSN REVDAT 2 24-FEB-09 3RHN 1 VERSN REVDAT 1 16-JUN-97 3RHN 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 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) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 7130 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) : 0.194 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 620 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 767 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 69 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 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 : 66 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) : 1.720 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.410 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 : GMPH.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 : GMPH.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RHN 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_1000179131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-94 REMARK 200 TEMPERATURE (KELVIN) : 277 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 27.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFINEMENT FROM MIR REMARK 200 STRUCTURE OF HINT-ADENOSINE REMARK 200 SOFTWARE USED: PROTSYS, X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: HINT-GMP, ISOMORPHOUS WITH HINT-ADENOSINE, WAS DETERMINED REMARK 200 BY REFINEMENT FROM THE HINT-ADENOSINE COORDINATES. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 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 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.27667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.55333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 54.55333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.27667 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: 5250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 -0.500000 -0.866025 0.000000 76.27500 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 44.03739 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.27667 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C GLU A 26 O HOH A 271 2.14 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 5GP A 201 DBREF 3RHN 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 5GP A 201 24 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 5GP C10 H14 N5 O8 P FORMUL 3 HOH *66(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 ARG A 12 PRO A 13 0 0.18 CISPEP 2 TRP A 123 PRO A 124 0 -0.03 SITE 1 HIT 3 HIS A 110 HIS A 112 HIS A 114 SITE 1 AC1 15 PHE A 19 PHE A 41 HIS A 42 ASP A 43 SITE 2 AC1 15 ILE A 44 LEU A 53 ASN A 99 GLY A 105 SITE 3 AC1 15 GLN A 106 SER A 107 VAL A 108 HIS A 112 SITE 4 AC1 15 HIS A 114 HOH A 219 HOH A 235 CRYST1 50.850 50.850 81.830 90.00 90.00 120.00 P 31 2 1 6 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 0.019666 0.011354 0.000000 0.00000 SCALE2 0.000000 0.022708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012220 0.00000