HEADER TRANSPORT PROTEIN 04-AUG-14 3WXQ TITLE SERIAL FEMTOSECOND X-RAY STRUCTURE OF HUMAN FATTY ACID-BINDING PROTEIN TITLE 2 TYPE-3 (FABP3) IN COMPLEX WITH STEARIC ACID (C18:0) DETERMINED USING TITLE 3 X-RAY FREE-ELECTRON LASER AT SACLA 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 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ANTIPARALLEL BETA BARREL, INTRACELLULAR TRANSPORT, HEART, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.MIZOHATA,M.SUZUKI,K.KAKINOUCHI,S.SUGIYAMA,M.MURATA,M.SUGAHARA, AUTHOR 2 E.NANGO,T.TANAKA,R.TANAKA,K.TONO,C.SONG,T.HATSUI,Y.JOTI,M.YABASHI, AUTHOR 3 S.IWATA REVDAT 4 08-NOV-23 3WXQ 1 REMARK REVDAT 3 14-MAR-18 3WXQ 1 SOURCE JRNL REMARK REVDAT 2 24-JAN-18 3WXQ 1 REMARK REVDAT 1 05-NOV-14 3WXQ 0 JRNL AUTH M.SUGAHARA,E.MIZOHATA,E.NANGO,M.SUZUKI,T.TANAKA,T.MASUDA, JRNL AUTH 2 R.TANAKA,T.SHIMAMURA,Y.TANAKA,C.SUNO,K.IHARA,D.PAN, JRNL AUTH 3 K.KAKINOUCHI,S.SUGIYAMA,M.MURATA,T.INOUE,K.TONO,C.SONG, JRNL AUTH 4 J.PARK,T.KAMESHIMA,T.HATSUI,Y.JOTI,M.YABASHI,S.IWATA JRNL TITL GREASE MATRIX AS A VERSATILE CARRIER OF PROTEINS FOR SERIAL JRNL TITL 2 CRYSTALLOGRAPHY JRNL REF NAT. METHODS V. 12 61 2015 JRNL REFN ESSN 1548-7105 JRNL PMID 25384243 JRNL DOI 10.1038/NMETH.3172 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17895 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 840 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 29.7058 - 2.9068 1.00 2980 162 0.2641 0.2736 REMARK 3 2 2.9068 - 2.3075 1.00 2880 121 0.1675 0.2088 REMARK 3 3 2.3075 - 2.0159 1.00 2826 135 0.1210 0.1837 REMARK 3 4 2.0159 - 1.8316 1.00 2801 159 0.1177 0.1781 REMARK 3 5 1.8316 - 1.7003 1.00 2786 141 0.1346 0.1976 REMARK 3 6 1.7003 - 1.6001 1.00 2782 122 0.1730 0.2604 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.160 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 : 0.017 1106 REMARK 3 ANGLE : 1.675 1490 REMARK 3 CHIRALITY : 0.076 178 REMARK 3 PLANARITY : 0.008 183 REMARK 3 DIHEDRAL : 13.522 425 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 3WXQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000096924. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 13231 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL3 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.23 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MPCCD OCTAL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18204 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3WVM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 73MM TRIS-HCL, 43% PEG400, 33MM NACL, REMARK 280 PH 8.0, BATCH METHOD, 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 16.85350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.32800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.42550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.32800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.85350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.42550 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 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 MET A 1 N ASP A 3 2.15 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 VAL A 2 -14.03 -26.49 REMARK 500 PHE A 58 -65.07 -100.13 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 STE A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WVM RELATED DB: PDB REMARK 900 RELATED ID: 3WUL RELATED DB: PDB REMARK 900 RELATED ID: 3WUM RELATED DB: PDB REMARK 900 RELATED ID: 3WXQ RELATED DB: PDB REMARK 900 RELATED ID: 3WXS RELATED DB: PDB REMARK 900 RELATED ID: 3WXT RELATED DB: PDB REMARK 900 RELATED ID: 3WXU RELATED DB: PDB REMARK 900 RELATED ID: 4W4Q RELATED DB: PDB DBREF 3WXQ A 1 133 UNP P05413 FABPH_HUMAN 1 133 SEQRES 1 A 133 MET VAL ASP ALA PHE LEU GLY THR TRP LYS LEU VAL ASP SEQRES 2 A 133 SER LYS ASN PHE ASP ASP TYR MET LYS SER LEU GLY VAL SEQRES 3 A 133 GLY PHE ALA THR ARG GLN VAL ALA SER MET THR LYS PRO SEQRES 4 A 133 THR THR ILE ILE GLU LYS ASN GLY ASP ILE LEU THR LEU SEQRES 5 A 133 LYS THR HIS SER THR PHE LYS ASN THR GLU ILE SER PHE SEQRES 6 A 133 LYS LEU GLY VAL GLU PHE ASP GLU THR THR ALA ASP ASP SEQRES 7 A 133 ARG LYS VAL LYS SER ILE VAL THR LEU ASP GLY GLY LYS SEQRES 8 A 133 LEU VAL HIS LEU GLN LYS TRP ASP GLY GLN GLU THR THR SEQRES 9 A 133 LEU VAL ARG GLU LEU ILE ASP GLY LYS LEU ILE LEU THR SEQRES 10 A 133 LEU THR HIS GLY THR ALA VAL CYS THR ARG THR TYR GLU SEQRES 11 A 133 LYS GLU ALA HET STE A 200 20 HETNAM STE STEARIC ACID FORMUL 2 STE C18 H36 O2 FORMUL 3 HOH *142(H2 O) HELIX 1 1 MET A 1 LEU A 6 5 6 HELIX 2 2 ASN A 16 GLY A 25 1 10 HELIX 3 3 GLY A 27 SER A 35 1 9 SHEET 1 A10 THR A 61 LYS A 66 0 SHEET 2 A10 ILE A 49 HIS A 55 -1 N LEU A 50 O PHE A 65 SHEET 3 A10 THR A 40 ASN A 46 -1 N ILE A 42 O LYS A 53 SHEET 4 A10 GLY A 7 LYS A 15 -1 N TRP A 9 O THR A 41 SHEET 5 A10 ALA A 123 GLU A 132 -1 O GLU A 132 N THR A 8 SHEET 6 A10 LYS A 113 HIS A 120 -1 N LEU A 116 O ARG A 127 SHEET 7 A10 GLN A 101 ILE A 110 -1 N GLU A 108 O ILE A 115 SHEET 8 A10 LYS A 91 TRP A 98 -1 N LEU A 92 O ARG A 107 SHEET 9 A10 LYS A 80 ASP A 88 -1 N THR A 86 O VAL A 93 SHEET 10 A10 PHE A 71 THR A 74 -1 N PHE A 71 O SER A 83 SITE 1 AC1 8 THR A 54 LYS A 59 ARG A 79 LEU A 116 SITE 2 AC1 8 ARG A 127 TYR A 129 HOH A 337 HOH A 367 CRYST1 33.707 54.851 70.656 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 0.029667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014153 0.00000