HEADER LIPID BINDING PROTEIN 27-APR-23 7FY9 TITLE CRYSTAL STRUCTURE OF HUMAN FABP4 BINDING SITE MUTATED TO THAT OF FABP5 TITLE 2 IN COMPLEX WITH 2-CYCLOPENTYL-4-(4-FLUOROPHENYL)-6-[1- TITLE 3 (METHOXYMETHYL)CYCLOPENTYL]-3-METHYL-5-(1H-TETRAZOL-5-YL)PYRIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, ADIPOCYTE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADIPOCYTE LIPID-BINDING PROTEIN,ALBP,ADIPOCYTE-TYPE FATTY COMPND 5 ACID-BINDING PROTEIN,A-FABP,AFABP,FATTY ACID-BINDING PROTEIN 4; COMPND 6 ENGINEERED: YES; COMPND 7 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: FABP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS LIPID BINDING PROTEIN, FATTY ACID BINDING PROTEIN, CYTOPLASM, LIPID- KEYWDS 2 BINDING, TRANSPORT, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.EHLER,J.BENZ,U.OBST,H.KUHNE,M.G.RUDOLPH REVDAT 2 03-APR-24 7FY9 1 REMARK REVDAT 1 14-JUN-23 7FY9 0 JRNL AUTH U.OBST,C.MAGNONE,B.KUHN,M.G.RUDOLPH JRNL TITL CRYSTAL STRUCTURE OF A HUMAN FABP4 BINDING SITE MUTATED TO JRNL TITL 2 THAT OF FABP5 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 12960 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) : 0.205 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.340 REMARK 3 FREE R VALUE TEST SET COUNT : 692 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 43.0187 - 2.9752 1.00 2617 144 0.1846 0.2361 REMARK 3 2 2.9752 - 2.3615 0.99 2472 165 0.2019 0.2923 REMARK 3 3 2.3615 - 2.0630 0.98 2424 131 0.2104 0.2556 REMARK 3 4 2.0630 - 1.8744 0.97 2374 121 0.2418 0.3669 REMARK 3 5 1.8744 - 1.7400 0.97 2381 131 0.2774 0.3515 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.37 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 : 0.013 1076 REMARK 3 ANGLE : 1.455 1452 REMARK 3 CHIRALITY : 0.078 167 REMARK 3 PLANARITY : 0.006 179 REMARK 3 DIHEDRAL : 16.801 403 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 7FY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1001405498. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000040 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12988 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 43.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.240 REMARK 200 R MERGE (I) : 0.17100 REMARK 200 R SYM (I) : 0.17100 REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.58 REMARK 200 R MERGE FOR SHELL (I) : 2.25800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.270 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: INHOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN IN 25MM TRIS/HCL PH 7.5 100MM REMARK 280 NACL, SEE ALSO PMID 27658368, PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.72750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.20450 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.72750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.20450 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 CYS A 1 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 OD2 ASP A 2 O HOH A 301 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 308 O HOH A 359 4554 2.14 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 ASP A 110 -120.17 48.99 REMARK 500 LYS A 120 -129.58 52.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FY9 A 0 131 UNP P15090 FABP4_HUMAN 1 132 SEQADV 7FY9 GLY A -3 UNP P15090 EXPRESSION TAG SEQADV 7FY9 SER A -2 UNP P15090 EXPRESSION TAG SEQADV 7FY9 HIS A -1 UNP P15090 EXPRESSION TAG SEQADV 7FY9 LEU A 23 UNP P15090 VAL 24 ENGINEERED MUTATION SEQADV 7FY9 MET A 32 UNP P15090 VAL 33 ENGINEERED MUTATION SEQADV 7FY9 GLY A 33 UNP P15090 ALA 34 ENGINEERED MUTATION SEQADV 7FY9 CYS A 40 UNP P15090 MET 41 ENGINEERED MUTATION SEQADV 7FY9 THR A 53 UNP P15090 SER 54 ENGINEERED MUTATION SEQADV 7FY9 LEU A 57 UNP P15090 PHE 58 ENGINEERED MUTATION SEQADV 7FY9 GLN A 93 UNP P15090 HIS 94 ENGINEERED MUTATION SEQADV 7FY9 CYS A 124 UNP P15090 SER 125 ENGINEERED MUTATION SEQRES 1 A 135 GLY SER HIS MET CYS ASP ALA PHE VAL GLY THR TRP LYS SEQRES 2 A 135 LEU VAL SER SER GLU ASN PHE ASP ASP TYR MET LYS GLU SEQRES 3 A 135 LEU GLY VAL GLY PHE ALA THR ARG LYS MET GLY GLY MET SEQRES 4 A 135 ALA LYS PRO ASN CYS ILE ILE SER VAL ASN GLY ASP VAL SEQRES 5 A 135 ILE THR ILE LYS THR GLU SER THR LEU LYS ASN THR GLU SEQRES 6 A 135 ILE SER PHE ILE LEU GLY GLN GLU PHE ASP GLU VAL THR SEQRES 7 A 135 ALA ASP ASP ARG LYS VAL LYS SER THR ILE THR LEU ASP SEQRES 8 A 135 GLY GLY VAL LEU VAL GLN VAL GLN LYS TRP ASP GLY LYS SEQRES 9 A 135 SER THR THR ILE LYS ARG LYS ARG GLU ASP ASP LYS LEU SEQRES 10 A 135 VAL VAL GLU CYS VAL MET LYS GLY VAL THR CYS THR ARG SEQRES 11 A 135 VAL TYR GLU ARG ALA HET K7C A 201 61 HET DMS A 202 4 HETNAM K7C (5P)-2-CYCLOPENTYL-4-(4-FLUOROPHENYL)-6-[1- HETNAM 2 K7C (METHOXYMETHYL)CYCLOPENTYL]-3-METHYL-5-(1H-TETRAZOL-5- HETNAM 3 K7C YL)PYRIDINE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 K7C C25 H30 F N5 O FORMUL 3 DMS C2 H6 O S FORMUL 4 HOH *67(H2 O) HELIX 1 AA1 ASN A 15 LEU A 23 1 9 HELIX 2 AA2 GLY A 26 ALA A 36 1 11 SHEET 1 AA110 THR A 60 ILE A 65 0 SHEET 2 AA110 VAL A 48 GLU A 54 -1 N ILE A 49 O PHE A 64 SHEET 3 AA110 ASN A 39 ASN A 45 -1 N ILE A 41 O LYS A 52 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O CYS A 40 SHEET 5 AA110 VAL A 122 ARG A 130 -1 O GLU A 129 N LYS A 9 SHEET 6 AA110 LYS A 112 MET A 119 -1 N VAL A 115 O ARG A 126 SHEET 7 AA110 LYS A 100 GLU A 109 -1 N LYS A 107 O VAL A 114 SHEET 8 AA110 VAL A 90 TRP A 97 -1 N TRP A 97 O LYS 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 VAL A 73 -1 N PHE A 70 O SER A 82 CRYST1 31.672 53.455 72.409 90.00 90.00 90.00 P 2 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 0.031574 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013810 0.00000