PDB Short entry for 1LFO HEADER INTRACELLULAR LIPID TRANSPORT PROTEIN 09-DEC-96 1LFO TITLE LIVER FATTY ACID BINDING PROTEIN-OLEATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIVER FATTY ACID BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LFABP; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: AMINO-TERMINAL INITIATOR METHIONINE AND MODIFIED COMPND 7 CYSTEINE 69 PRESENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: LIVER; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K12 H1; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJBL2 KEYWDS INTRACELLULAR LIPID TRANSPORT PROTEIN, FATTY ACID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.THOMPSON,N.WINTER,D.TERWEY,J.BRATT,L.BANASZAK REVDAT 3 09-AUG-23 1LFO 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1LFO 1 VERSN REVDAT 1 16-JUN-97 1LFO 0 JRNL AUTH J.THOMPSON,N.WINTER,D.TERWEY,J.BRATT,L.BANASZAK JRNL TITL THE CRYSTAL STRUCTURE OF THE LIVER FATTY ACID-BINDING JRNL TITL 2 PROTEIN. A COMPLEX WITH TWO BOUND OLEATES. JRNL REF J.BIOL.CHEM. V. 272 7140 1997 JRNL REFN ISSN 0021-9258 JRNL PMID 9054409 JRNL DOI 10.1074/JBC.272.11.7140 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 7475 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) : 0.202 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 396 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 30 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 153 REMARK 3 BIN R VALUE (WORKING SET) : 0.4600 REMARK 3 BIN FREE R VALUE : 0.4500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 12 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.131 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.90 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) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.530 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 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) : 1.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.700 ; 2.500 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : OLEATE.PAR REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : OLEATE.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LFO 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_1000174699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-91 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 5.6 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 : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8640 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.3 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 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) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: SUPERIMPOSED POLYALANINE COMPOSITE STRUCTURE OF REMARK 200 1ADL, 1CBR, 1CRB, 1OPB, 1IFC, 1HMR REMARK 200 REMARK 200 REMARK: DATA IN THE 2.3 - 2.1 ANGSTROM RANGE WAS NOT USED DUE TO REMARK 200 ITS POOR QUALITY. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOR DIFFUSION REMARK 280 EXPERIMENT 1 ML WELL: 3 M AMMONIUM SULFATE, 200 MM LISO4, 100 MM REMARK 280 CITRATE, AT A PH OF 5.6 STOCK: 13 MG/ML LFABP-OLEATE COMPLEX 10 REMARK 280 MICROLITER DROP: 1:1 MIXTURE OF STOCK AND WELL, VAPOR DIFFUSION - REMARK 280 HANGING DROP, PH 5.6, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 29.76667 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 14.88333 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 14.88333 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 29.76667 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: 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 ASN A 2 114.11 66.88 REMARK 500 GLU A 26 -59.93 -24.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEO A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 131 DBREF 1LFO A 1 127 UNP P02692 FABPL_RAT 1 127 SEQADV 1LFO SMC A 69 UNP P02692 CYS 69 MODIFIED RESIDUE SEQRES 1 A 128 ACE MET ASN PHE SER GLY LYS TYR GLN VAL GLN SER GLN SEQRES 2 A 128 GLU ASN PHE GLU PRO PHE MET LYS ALA MET GLY LEU PRO SEQRES 3 A 128 GLU ASP LEU ILE GLN LYS GLY LYS ASP ILE LYS GLY VAL SEQRES 4 A 128 SER GLU ILE VAL HIS GLU GLY LYS LYS VAL LYS LEU THR SEQRES 5 A 128 ILE THR TYR GLY SER LYS VAL ILE HIS ASN GLU PHE THR SEQRES 6 A 128 LEU GLY GLU GLU SMC GLU LEU GLU THR MET THR GLY GLU SEQRES 7 A 128 LYS VAL LYS ALA VAL VAL LYS MET GLU GLY ASP ASN LYS SEQRES 8 A 128 MET VAL THR THR PHE LYS GLY ILE LYS SER VAL THR GLU SEQRES 9 A 128 PHE ASN GLY ASP THR ILE THR ASN THR MET THR LEU GLY SEQRES 10 A 128 ASP ILE VAL TYR LYS ARG VAL SER LYS ARG ILE MODRES 1LFO SMC A 69 CYS S-METHYLCYSTEINE HET ACE A 0 3 HET SMC A 69 7 HET OLA A 128 20 HET OLA A 129 20 HET BEO A 130 6 HET UNX A 131 1 HETNAM ACE ACETYL GROUP HETNAM SMC S-METHYLCYSTEINE HETNAM OLA OLEIC ACID HETNAM BEO BUTENOIC ACID HETNAM UNX UNKNOWN ATOM OR ION FORMUL 1 ACE C2 H4 O FORMUL 1 SMC C4 H9 N O2 S FORMUL 2 OLA 2(C18 H34 O2) FORMUL 4 BEO C4 H6 O2 FORMUL 5 UNX X FORMUL 6 HOH *61(H2 O) HELIX 1 1 PHE A 15 MET A 22 1 8 HELIX 2 2 GLU A 26 ASP A 34 1 9 SHEET 1 A 9 LYS A 57 THR A 64 0 SHEET 2 A 9 LYS A 47 TYR A 54 -1 N TYR A 54 O LYS A 57 SHEET 3 A 9 VAL A 38 GLU A 44 -1 N GLU A 44 O LYS A 47 SHEET 4 A 9 GLY A 5 GLU A 13 -1 N TYR A 7 O SER A 39 SHEET 5 A 9 ILE A 118 ILE A 127 -1 N ILE A 127 O LYS A 6 SHEET 6 A 9 THR A 108 LEU A 115 -1 N LEU A 115 O ILE A 118 SHEET 7 A 9 ILE A 98 ASN A 105 -1 N ASN A 105 O THR A 108 SHEET 8 A 9 LYS A 90 PHE A 95 -1 N PHE A 95 O ILE A 98 SHEET 9 A 9 LYS A 84 GLU A 86 -1 N GLU A 86 O LYS A 90 LINK C ACE A 0 N MET A 1 1555 1555 1.33 LINK C GLU A 68 N SMC A 69 1555 1555 1.33 LINK C SMC A 69 N GLU A 70 1555 1555 1.33 SITE 1 AC1 9 LYS A 31 GLY A 32 TYR A 54 GLY A 55 SITE 2 AC1 9 SER A 56 LYS A 57 ASP A 88 ARG A 122 SITE 3 AC1 9 OLA A 129 SITE 1 AC2 10 SER A 39 PHE A 63 GLU A 72 MET A 74 SITE 2 AC2 10 THR A 102 ARG A 122 OLA A 128 UNX A 131 SITE 3 AC2 10 HOH A 179 HOH A 181 SITE 1 AC3 4 ASN A 14 PHE A 15 GLU A 16 PRO A 17 SITE 1 AC4 2 ILE A 59 OLA A 129 CRYST1 83.890 83.890 44.650 90.00 90.00 120.00 P 32 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 0.011920 0.006882 0.000000 0.00000 SCALE2 0.000000 0.013764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022396 0.00000 HETATM 1 C ACE A 0 30.449 6.858 35.831 1.00 85.66 C HETATM 2 O ACE A 0 29.425 7.432 35.402 1.00 88.15 O HETATM 3 CH3 ACE A 0 31.072 5.721 34.975 1.00 89.65 C