HEADER ACYL-COENZYME A BINDING PROTEIN 12-APR-01 1HB6 TITLE STRUCTURE OF BOVINE ACYL-COA BINDING PROTEIN IN ORTHORHOMBIC CRYSTAL TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-COA BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACBP, DIAZEPAM BINDING INHIBITOR, DBI ENDOZEPINE, EP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 4 ORGANISM_COMMON: BOVINE; SOURCE 5 ORGANISM_TAXID: 9913 KEYWDS ACYL-COENZYME A BINDING PROTEIN, ACYL-COA, BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.ZOU,G.J.KLEYWEGT,T.BERGFORS,J.KNUDSEN,T.A.JONES REVDAT 4 13-DEC-23 1HB6 1 REMARK LINK REVDAT 3 24-FEB-09 1HB6 1 VERSN REVDAT 2 29-NOV-04 1HB6 1 REMARK REVDAT 1 11-MAR-02 1HB6 0 JRNL AUTH D.M.F.VAN AALTEN,K.G.MILNE,J.Y.ZOU,G.J.KLEYWEGT,T.BERGFORS, JRNL AUTH 2 M.A.J.FERGUSON,J.KNUDSEN,T.A.JONES JRNL TITL BINDING SITE DIFFERENCES REVEALED BY CRYSTAL STRUCTURES OF JRNL TITL 2 PLASMODIUM FALCIPARUM AND BOVINE ACYL-COA BINDING PROTEIN JRNL REF J.MOL.BIOL. V. 309 181 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11491287 JRNL DOI 10.1006/JMBI.2001.4749 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 279496.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 6394 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 SET) : 0.200 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 647 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 645 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 79 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.83000 REMARK 3 B22 (A**2) : -2.90000 REMARK 3 B33 (A**2) : 0.08000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.650 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.460 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.130 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.140 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 38.55 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1HB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-01. REMARK 100 THE DEPOSITION ID IS D_1290006096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-91 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.50 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MULTIWIRE UCSD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD REMARK 200 DATA SCALING SOFTWARE : UCSD REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6473 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.07600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2ABD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8000, 5MMCDCL2, 10MM HEPES REMARK 280 PH7.5, PH 7.50 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 13.02500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.91500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.91500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.02500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.39000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 MAY FUNCTION AS AN INTRACELLULAR CARRIER OF ACYL-COA ESTERS. REMARK 400 IT ALSO DISPLACES DIAZEPAM FROM THE BENZODIAZEPINE (BZD) REMARK 400 RECOGNITION SITE LOCATED ON THE GABA TYPE A RECEPTOR. REMARK 400 IT IS THEREFORE POSSIBLE THAT IT MODULATES THE ACTION OF THE REMARK 400 GABA RECEPTOR. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 200 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 GLU A 42 OE1 95.7 REMARK 620 3 GLU A 42 OE2 139.6 50.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ACA RELATED DB: PDB REMARK 900 ACYL-COENZYME A BINDING PROTEIN (ACBP) COMPLEX WITH PALMITOYL- REMARK 900 COENZYME A (NMR, 20 STRUCTURES) REMARK 900 RELATED ID: 2ABD RELATED DB: PDB REMARK 900 ACYL-COENZYME A BINDING PROTEIN (ACBP) REMARK 900 RELATED ID: 1HB8 RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE ACYL-COA BINDING PROTEIN IN TETRAGONAL CRYSTAL REMARK 900 FORM DBREF 1HB6 A 1 86 UNP P07107 ACBP_BOVIN 1 86 SEQRES 1 A 86 SER GLN ALA GLU PHE ASP LYS ALA ALA GLU GLU VAL LYS SEQRES 2 A 86 HIS LEU LYS THR LYS PRO ALA ASP GLU GLU MET LEU PHE SEQRES 3 A 86 ILE TYR SER HIS TYR LYS GLN ALA THR VAL GLY ASP ILE SEQRES 4 A 86 ASN THR GLU ARG PRO GLY MET LEU ASP PHE LYS GLY LYS SEQRES 5 A 86 ALA LYS TRP ASP ALA TRP ASN GLU LEU LYS GLY THR SER SEQRES 6 A 86 LYS GLU ASP ALA MET LYS ALA TYR ILE ASP LYS VAL GLU SEQRES 7 A 86 GLU LEU LYS LYS LYS TYR GLY ILE HET CD A 200 1 HETNAM CD CADMIUM ION FORMUL 2 CD CD 2+ FORMUL 3 HOH *60(H2 O) HELIX 1 1 SER A 1 VAL A 12 1 12 HELIX 2 2 LYS A 13 LEU A 15 5 3 HELIX 3 3 ALA A 20 VAL A 36 1 17 HELIX 4 4 ASP A 48 LEU A 61 1 14 HELIX 5 5 SER A 65 GLY A 85 1 21 LINK NE2 HIS A 14 CD CD A 200 1555 1555 2.33 LINK OE1 GLU A 42 CD CD A 200 2754 1555 2.67 LINK OE2 GLU A 42 CD CD A 200 2754 1555 2.50 SITE 1 AC1 2 HIS A 14 GLU A 42 CRYST1 26.050 54.780 65.830 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 0.038388 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015191 0.00000