HEADER LIPID BINDING PROTEIN 12-JAN-16 5B29 TITLE THE 1.28A STRUCTURE OF HUMAN FABP3 F16V MUTANT COMPLEXED WITH PALMITIC TITLE 2 ACID AT ROOM TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, HEART; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FATTY ACID-BINDING PROTEIN 3,HEART-TYPE FATTY ACID-BINDING COMPND 5 PROTEIN,H-FABP,MAMMARY-DERIVED GROWTH INHIBITOR,MDGI,MUSCLE FATTY COMPND 6 ACID-BINDING PROTEIN,M-FABP; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FABP3, FABP11, MDGI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID BINDING PROTEIN, COMPLEX, PALMITIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR D.MATSUOKA,S.SUGIYAMA,K.KAKINOUCHI,M.NIIYAMA,M.MURATA,S.MATSUOKA REVDAT 3 20-MAR-24 5B29 1 REMARK REVDAT 2 26-FEB-20 5B29 1 REMARK REVDAT 1 18-JAN-17 5B29 0 JRNL AUTH D.MATSUOKA,S.SUGIYAMA,K.KAKINOUCHI,M.NIIYAMA,M.MURATA, JRNL AUTH 2 S.MATSUOKA JRNL TITL THE 1.28A STRUCTURE OF HUMAN FABP3 F16V MUTANT COMPLEXED JRNL TITL 2 WITH PALMITIC ACID AT ROOM TEMPERATURE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1786 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 31.0812 - 3.0074 0.98 2759 146 0.1480 0.1816 REMARK 3 2 3.0074 - 2.3873 1.00 2666 146 0.1439 0.1718 REMARK 3 3 2.3873 - 2.0856 1.00 2651 134 0.1121 0.1382 REMARK 3 4 2.0856 - 1.8950 1.00 2599 154 0.0976 0.1338 REMARK 3 5 1.8950 - 1.7591 1.00 2624 126 0.1041 0.1785 REMARK 3 6 1.7591 - 1.6554 1.00 2605 135 0.1127 0.1635 REMARK 3 7 1.6554 - 1.5725 1.00 2564 153 0.1692 0.2082 REMARK 3 8 1.5725 - 1.5041 1.00 2584 136 0.2769 0.3549 REMARK 3 9 1.5041 - 1.4462 1.00 2573 150 0.3551 0.4195 REMARK 3 10 1.4462 - 1.3963 1.00 2588 134 0.4124 0.5041 REMARK 3 11 1.3963 - 1.3526 1.00 2615 117 0.3741 0.4406 REMARK 3 12 1.3526 - 1.3140 1.00 2585 123 0.3388 0.4581 REMARK 3 13 1.3140 - 1.2794 0.98 2508 132 0.3189 0.3537 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.610 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 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 : 0.009 1227 REMARK 3 ANGLE : 1.014 1678 REMARK 3 CHIRALITY : 0.093 204 REMARK 3 PLANARITY : 0.005 210 REMARK 3 DIHEDRAL : 16.671 487 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 5B29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1300000396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 296 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 31.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.74500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH8.0), 45-55% (V/V) REMARK 280 PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 27.61000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.27750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.50900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.27750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.61000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.50900 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 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 431 DISTANCE = 6.15 ANGSTROMS 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 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WBG RELATED DB: PDB REMARK 900 THE STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH 1-ANILINONAPHTALENE-8- REMARK 900 SULPHONIC ACID. REMARK 900 RELATED ID: 4TJZ RELATED DB: PDB REMARK 900 THE 0.87A STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH CAPRIC ACID. REMARK 900 RELATED ID: 4TKB RELATED DB: PDB REMARK 900 THE 0.86A STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH LEURIC ACID. REMARK 900 RELATED ID: 4TKH RELATED DB: PDB REMARK 900 THE 0.93A STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH MYRISTIC ACID. REMARK 900 RELATED ID: 4TKJ RELATED DB: PDB REMARK 900 THE 0.87A STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH PALMITIC ACID. REMARK 900 RELATED ID: 3WVM RELATED DB: PDB REMARK 900 THE 0.88A STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH STEARIC ACID. REMARK 900 RELATED ID: 4WBK RELATED DB: PDB REMARK 900 THE 1.37A STRUCTURE OF FABP3 PROTEIN COMPLEXED WITH STEARIC ACID. REMARK 900 RELATED ID: 5B27 RELATED DB: PDB REMARK 900 THE 1.02A STRUCTURE OF HUMAN FABP3 M20S MUTANT COMPLEXED WITH REMARK 900 PALMITIC ACID REMARK 900 RELATED ID: 5B28 RELATED DB: PDB REMARK 900 THE 0.90A STRUCTURE OF HUMAN FABP3 F16V MUTANT COMPLEXED WITH REMARK 900 PALMITIC ACID. DBREF 5B29 A 1 132 UNP P05413 FABPH_HUMAN 2 133 SEQADV 5B29 VAL A 16 UNP P05413 PHE 17 ENGINEERED MUTATION SEQRES 1 A 132 VAL ASP ALA PHE LEU GLY THR TRP LYS LEU VAL ASP SER SEQRES 2 A 132 LYS ASN VAL ASP ASP TYR MET LYS SER LEU GLY VAL GLY SEQRES 3 A 132 PHE ALA THR ARG GLN VAL ALA SER MET THR LYS PRO THR SEQRES 4 A 132 THR ILE ILE GLU LYS ASN GLY ASP ILE LEU THR LEU LYS SEQRES 5 A 132 THR HIS SER THR PHE LYS ASN THR GLU ILE SER PHE LYS SEQRES 6 A 132 LEU GLY VAL GLU PHE ASP GLU THR THR ALA ASP ASP ARG SEQRES 7 A 132 LYS VAL LYS SER ILE VAL THR LEU ASP GLY GLY LYS LEU SEQRES 8 A 132 VAL HIS LEU GLN LYS TRP ASP GLY GLN GLU THR THR LEU SEQRES 9 A 132 VAL ARG GLU LEU ILE ASP GLY LYS LEU ILE LEU THR LEU SEQRES 10 A 132 THR HIS GLY THR ALA VAL CYS THR ARG THR TYR GLU LYS SEQRES 11 A 132 GLU ALA HET PLM A 200 18 HETNAM PLM PALMITIC ACID FORMUL 2 PLM C16 H32 O2 FORMUL 3 HOH *131(H2 O) HELIX 1 AA1 VAL A 1 LEU A 5 5 5 HELIX 2 AA2 ASN A 15 GLY A 24 1 10 HELIX 3 AA3 GLY A 26 THR A 36 1 11 SHEET 1 AA110 THR A 60 LYS A 65 0 SHEET 2 AA110 ILE A 48 HIS A 54 -1 N LEU A 49 O PHE A 64 SHEET 3 AA110 THR A 39 ASN A 45 -1 N THR A 39 O HIS A 54 SHEET 4 AA110 GLY A 6 LYS A 14 -1 N TRP A 8 O THR A 40 SHEET 5 AA110 ALA A 122 GLU A 131 -1 O GLU A 131 N THR A 7 SHEET 6 AA110 LYS A 112 HIS A 119 -1 N LEU A 115 O ARG A 126 SHEET 7 AA110 GLN A 100 ILE A 109 -1 N GLU A 107 O ILE A 114 SHEET 8 AA110 LYS A 90 TRP A 97 -1 N TRP A 97 O GLN A 100 SHEET 9 AA110 LYS A 79 ASP A 87 -1 N THR A 85 O VAL A 92 SHEET 10 AA110 PHE A 70 THR A 73 -1 N PHE A 70 O SER A 82 SITE 1 AC1 5 LEU A 115 ARG A 126 TYR A 128 HOH A 315 SITE 2 AC1 5 HOH A 346 CRYST1 55.220 71.018 34.555 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 0.018109 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028939 0.00000