HEADER LIPID BINDING PROTEIN 19-MAY-21 7EUW TITLE X-RAY STRUCTURE OF HIGH-STRENGTH HYDROGEL-GROWN FABP3 CRYSTAL SOAKED TITLE 2 IN 50% DMSO SOLUTION CONTAINING 4-[2-[1-(4-BROMOPHENYL)-5-PHENYL-1H- TITLE 3 PYRAZOL-3-YL]PHENOXY] (HA174) 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FABP, COMPLEX, BINDING PROTEIN, HA174, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SUGIYAMA,K.KAKINOUCHI,R.NAKANO,S.MATSUOKA,H.TSUCHIKAWA,M.SONOYAMA, AUTHOR 2 Y.INOUE,F.HAYASHI,M.MURATA REVDAT 2 29-NOV-23 7EUW 1 REMARK REVDAT 1 25-MAY-22 7EUW 0 JRNL AUTH S.SUGIYAMA,K.KAKINOUCHI,S.MATSUOKA,H.TSUCHIKAWA,M.SONOYAMA, JRNL AUTH 2 Y.INOUE,F.HAYASHI,M.MURATA JRNL TITL X-RAY STRUCTURE OF THE HUMAN HEART FATTY ACID-BINDING JRNL TITL 2 PROTEIN COMPLEXED WITH JRNL TITL 3 4-[2-[1-(4-BROMOPHENYL)-5-PHENYL-1H-PYRAZOL-3-YL]PHENOXY] JRNL TITL 4 (HA176) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 16708 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 + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 914 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 943 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1031 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 0.70000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.984 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1243 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1192 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1701 ; 1.791 ; 1.684 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2781 ; 1.403 ; 1.615 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 6.116 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;40.080 ;24.082 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 238 ;12.787 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;12.822 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 168 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1421 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 252 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 612 ; 1.362 ; 1.586 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 613 ; 1.362 ; 1.588 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 792 ; 2.043 ; 2.374 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 792 ; 2.044 ; 2.374 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 631 ; 2.092 ; 1.780 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 623 ; 2.073 ; 1.784 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 903 ; 3.150 ; 2.593 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1381 ; 4.884 ;19.681 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1321 ; 4.532 ;18.822 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7EUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300022294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.80000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 88.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 3WVM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH8.5), 50% PEG 400, REMARK 280 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 27.27650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.25100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.21050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.25100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.27650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.21050 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 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL 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 ALA A 132 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 MET A 0 CG SD CE REMARK 470 GLU A 131 CG CD OE1 OE2 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 494 DISTANCE = 6.33 ANGSTROMS DBREF 7EUW A 0 132 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 JEC A 201 31 HET SO3 A 202 4 HET SO3 A 203 4 HETNAM JEC 4-[2-[1-(4-BROMOPHENYL)-5-PHENYL-PYRAZOL-3- HETNAM 2 JEC YL]PHENOXY]BUTANOIC ACID HETNAM SO3 SULFITE ION FORMUL 2 JEC C25 H21 BR N2 O3 FORMUL 3 SO3 2(O3 S 2-) FORMUL 5 HOH *194(H2 O) HELIX 1 AA1 VAL A 1 LEU A 5 5 5 HELIX 2 AA2 ASN A 15 LEU A 23 1 9 HELIX 3 AA3 GLY A 26 SER A 34 1 9 SHEET 1 AA110 ASN A 59 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 LYS A 130 -1 O THR A 127 N VAL A 11 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 VAL A 105 O THR A 116 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 GLU A 72 O VAL A 80 CRYST1 54.553 70.421 34.502 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 0.018331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014200 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028984 0.00000