PDB Short entry for 1ICM HEADER BINDING PROTEIN(FATTY ACID) 20-SEP-93 1ICM TITLE ESCHERICHIA COLI-DERIVED RAT INTESTINAL FATTY ACID BINDING PROTEIN TITLE 2 WITH BOUND MYRISTATE AT 1.5 A RESOLUTION AND I-FABPARG106-->GLN WITH TITLE 3 BOUND OLEATE AT 1.74 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTESTINAL FATTY ACID BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116 KEYWDS BINDING PROTEIN(FATTY ACID) EXPDTA X-RAY DIFFRACTION AUTHOR J.C.EADS,J.C.SACCHETTINI,A.KROMMINGA,J.I.GORDON REVDAT 4 07-FEB-24 1ICM 1 REMARK REVDAT 3 29-NOV-17 1ICM 1 HELIX REVDAT 2 24-FEB-09 1ICM 1 VERSN REVDAT 1 31-JAN-94 1ICM 0 JRNL AUTH J.EADS,J.C.SACCHETTINI,A.KROMMINGA,J.I.GORDON JRNL TITL ESCHERICHIA COLI-DERIVED RAT INTESTINAL FATTY ACID BINDING JRNL TITL 2 PROTEIN WITH BOUND MYRISTATE AT 1.5 A RESOLUTION AND JRNL TITL 3 I-FABPARG106-->GLN WITH BOUND OLEATE AT 1.74 A RESOLUTION. JRNL REF J.BIOL.CHEM. V. 268 26375 1993 JRNL REFN ISSN 0021-9258 JRNL PMID 8253762 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.SCAPIN,J.I.GORDON,J.C.SACCHETTINI REMARK 1 TITL REFINEMENT OF THE STRUCTURE OF RECOMBINANT RAT INTESTINAL REMARK 1 TITL 2 FATTY ACID-BINDING APOPROTEIN AT 1.2 ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 267 4253 1992 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1057 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.690 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ICM 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_1000174103. 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 <I/SIGMA(I)> 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 <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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.90000 REMARK 290 SMTRY3 2 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 15 CD GLU A 15 OE2 0.073 REMARK 500 GLU A 19 CD GLU A 19 OE1 0.067 REMARK 500 GLU A 43 CD GLU A 43 OE2 0.069 REMARK 500 GLU A 101 CD GLU A 101 OE1 0.068 REMARK 500 GLU A 107 CD GLU A 107 OE1 0.079 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 3 CB - CG - OD2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ASP A 67 CB - CG - OD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 ASP A 74 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 GLU A 85 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 95 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ARG A 56 -178.89 -171.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FA1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR A 133 DBREF 1ICM A 1 131 UNP P02693 FABPI_RAT 1 131 SEQRES 1 A 131 ALA PHE ASP GLY THR TRP LYS VAL ASP ARG ASN GLU ASN SEQRES 2 A 131 TYR GLU LYS PHE MET GLU LYS MET GLY ILE ASN VAL VAL SEQRES 3 A 131 LYS ARG LYS LEU GLY ALA HIS ASP ASN LEU LYS LEU THR SEQRES 4 A 131 ILE THR GLN GLU GLY ASN LYS PHE THR VAL LYS GLU SER SEQRES 5 A 131 SER ASN PHE ARG ASN ILE ASP VAL VAL PHE GLU LEU GLY SEQRES 6 A 131 VAL ASP PHE ALA TYR SER LEU ALA ASP GLY THR GLU LEU SEQRES 7 A 131 THR GLY THR TRP THR MET GLU GLY ASN LYS LEU VAL GLY SEQRES 8 A 131 LYS PHE LYS ARG VAL ASP ASN GLY LYS GLU LEU ILE ALA SEQRES 9 A 131 VAL ARG GLU ILE SER GLY ASN GLU LEU ILE GLN THR TYR SEQRES 10 A 131 THR TYR GLU GLY VAL GLU ALA LYS ARG ILE PHE LYS LYS SEQRES 11 A 131 GLU HET MYR A 133 16 HETNAM MYR MYRISTIC ACID FORMUL 2 MYR C14 H28 O2 FORMUL 3 HOH *130(H2 O) HELIX 1 A1 TYR A 14 LYS A 20 1 7 HELIX 2 A2 VAL A 25 HIS A 33 1 9 SHEET 1 A 6 ALA A 1 GLU A 12 0 SHEET 2 A 6 ASP A 34 GLN A 42 -1 N ILE A 40 O GLY A 4 SHEET 3 A 6 PHE A 47 SER A 52 -1 N THR A 48 O THR A 41 SHEET 4 A 6 ASN A 57 PHE A 62 -1 N VAL A 60 O VAL A 49 SHEET 5 A 6 ASP A 67 SER A 71 0 SHEET 6 A 6 THR A 76 GLY A 80 -1 N LEU A 78 O TYR A 70 SHEET 1 B 5 THR A 81 MET A 84 0 SHEET 2 B 5 LEU A 89 LYS A 94 -1 N VAL A 90 O THR A 83 SHEET 3 B 5 LYS A 100 ILE A 108 -1 N ALA A 104 O GLY A 91 SHEET 4 B 5 LEU A 113 THR A 118 -1 N THR A 116 O VAL A 105 SHEET 5 B 5 GLU A 123 GLU A 131 -1 N ARG A 126 O GLN A 115 SITE 1 FA1 6 ARG A 106 TRP A 82 GLN A 115 TYR A 70 SITE 2 FA1 6 TYR A 117 PHE A 55 SITE 1 AC1 5 TYR A 14 PHE A 62 TRP A 82 ARG A 106 SITE 2 AC1 5 HOH A 170 CRYST1 36.050 51.800 31.480 90.00 92.00 90.00 P 1 21 1 2 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 0.027739 0.000000 0.000969 0.00000 SCALE2 0.000000 0.019305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031786 0.00000