HEADER LIPID BINDING PROTEIN 11-JUL-11 3STK TITLE CRYSTAL STRUCTURE OF HUMAN LFABP COMPLEX WITH TWO MOLECULES OF TITLE 2 PALMITIC ACID (HOLO-LFABP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, LIVER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FATTY ACID-BINDING PROTEIN 1, LIVER-TYPE FATTY ACID-BINDING COMPND 5 PROTEIN, L-FABP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FABP1, FABPL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A(+) KEYWDS LFABP, PALMITIC ACID, FATTY ACID BINDING, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SHARMA,A.SHARMA REVDAT 3 20-MAR-24 3STK 1 REMARK SEQADV REVDAT 2 08-NOV-17 3STK 1 REMARK REVDAT 1 10-AUG-11 3STK 0 JRNL AUTH A.SHARMA,A.SHARMA JRNL TITL FATTY ACID INDUCED REMODELING WITHIN THE HUMAN LIVER FATTY JRNL TITL 2 ACID BINDING PROTEIN JRNL REF J.BIOL.CHEM. 2011 JRNL REFN ESSN 1083-351X JRNL PMID 21757748 JRNL DOI 10.1074/JBC.M111.270165 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 18190 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 934 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.1960 - 2.9640 0.90 2546 119 0.1910 0.1848 REMARK 3 2 2.9640 - 2.3532 0.98 2603 143 0.1971 0.2575 REMARK 3 3 2.3532 - 2.0559 0.94 2510 127 0.2006 0.2059 REMARK 3 4 2.0559 - 1.8680 0.94 2456 121 0.2050 0.2319 REMARK 3 5 1.8680 - 1.7341 0.94 2448 142 0.2224 0.2854 REMARK 3 6 1.7341 - 1.6319 0.93 2404 140 0.3245 0.3630 REMARK 3 7 1.6319 - 1.5502 0.89 2289 142 0.4196 0.4659 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 45.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29470 REMARK 3 B22 (A**2) : 0.06290 REMARK 3 B33 (A**2) : -0.35770 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1046 REMARK 3 ANGLE : 1.022 1388 REMARK 3 CHIRALITY : 0.066 159 REMARK 3 PLANARITY : 0.003 174 REMARK 3 DIHEDRAL : 16.677 412 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3STK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 MICROMAX-007 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18383 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M POTASSIUM BROMIDE, 30% REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEG MME) 2000, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 15.14150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.43050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.54850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.43050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.14150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.54850 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: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 GLY A 0 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 THR A 129 OG1 CG2 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 O HOH A 188 O HOH A 197 1.93 REMARK 500 N SER A 1 O HOH A 210 1.94 REMARK 500 O HOH A 160 O HOH A 181 2.02 REMARK 500 O HOH A 152 O HOH A 196 2.06 REMARK 500 O HOH A 176 O HOH A 224 2.09 REMARK 500 O HOH A 191 O HOH A 336 2.10 REMARK 500 O HOH A 214 O HOH A 216 2.13 REMARK 500 O HOH A 135 O HOH A 340 2.13 REMARK 500 O HOH A 182 O HOH A 276 2.18 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 PLM A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3STM RELATED DB: PDB REMARK 900 RELATED ID: 3STN RELATED DB: PDB DBREF 3STK A 2 127 UNP P07148 FABPL_HUMAN 2 127 SEQADV 3STK MET A -2 UNP P07148 EXPRESSION TAG SEQADV 3STK ALA A -1 UNP P07148 EXPRESSION TAG SEQADV 3STK GLY A 0 UNP P07148 EXPRESSION TAG SEQADV 3STK SER A 1 UNP P07148 EXPRESSION TAG SEQADV 3STK GLY A 128 UNP P07148 EXPRESSION TAG SEQADV 3STK THR A 129 UNP P07148 EXPRESSION TAG SEQRES 1 A 132 MET ALA GLY SER SER PHE SER GLY LYS TYR GLN LEU GLN SEQRES 2 A 132 SER GLN GLU ASN PHE GLU ALA PHE MET LYS ALA ILE GLY SEQRES 3 A 132 LEU PRO GLU GLU LEU ILE GLN LYS GLY LYS ASP ILE LYS SEQRES 4 A 132 GLY VAL SER GLU ILE VAL GLN ASN GLY LYS HIS PHE LYS SEQRES 5 A 132 PHE THR ILE THR ALA GLY SER LYS VAL ILE GLN ASN GLU SEQRES 6 A 132 PHE THR VAL GLY GLU GLU CYS GLU LEU GLU THR MET THR SEQRES 7 A 132 GLY GLU LYS VAL LYS THR VAL VAL GLN LEU GLU GLY ASP SEQRES 8 A 132 ASN LYS LEU VAL THR THR PHE LYS ASN ILE LYS SER VAL SEQRES 9 A 132 THR GLU LEU ASN GLY ASP ILE ILE THR ASN THR MET THR SEQRES 10 A 132 LEU GLY ASP ILE VAL PHE LYS ARG ILE SER LYS ARG ILE SEQRES 11 A 132 GLY THR HET PLM A 130 18 HET PLM A 131 18 HETNAM PLM PALMITIC ACID FORMUL 2 PLM 2(C16 H32 O2) FORMUL 4 HOH *224(H2 O) HELIX 1 1 ASN A 14 GLY A 23 1 10 HELIX 2 2 PRO A 25 LYS A 33 1 9 SHEET 1 A 9 LYS A 57 THR A 64 0 SHEET 2 A 9 HIS A 47 ALA A 54 -1 N ALA A 54 O LYS A 57 SHEET 3 A 9 VAL A 38 ASN A 44 -1 N VAL A 42 O LYS A 49 SHEET 4 A 9 GLY A 5 GLU A 13 -1 N GLY A 5 O ILE A 41 SHEET 5 A 9 ILE A 118 ARG A 126 -1 O ILE A 123 N GLN A 10 SHEET 6 A 9 ILE A 108 LEU A 115 -1 N MET A 113 O PHE A 120 SHEET 7 A 9 ILE A 98 ASN A 105 -1 N ASN A 105 O ILE A 108 SHEET 8 A 9 LYS A 90 PHE A 95 -1 N LEU A 91 O THR A 102 SHEET 9 A 9 GLN A 84 LEU A 85 -1 N GLN A 84 O VAL A 92 SHEET 1 B 2 GLU A 68 GLU A 72 0 SHEET 2 B 2 LYS A 78 VAL A 82 -1 O THR A 81 N CYS A 69 SITE 1 AC1 8 SER A 39 ILE A 52 GLU A 72 THR A 102 SITE 2 AC1 8 ASN A 111 ARG A 122 PLM A 131 HOH A 227 SITE 1 AC2 5 ALA A 54 SER A 56 ASN A 111 ARG A 122 SITE 2 AC2 5 PLM A 130 CRYST1 30.283 57.097 74.861 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 0.033022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013358 0.00000