HEADER LIPID BINDING PROTEIN 27-MAR-23 8IVF TITLE FABP7 COMPLEXED WITH 25-HC COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, BRAIN; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: BRAIN LIPID-BINDING PROTEIN,BLBP,BRAIN-TYPE FATTY ACID- COMPND 5 BINDING PROTEIN,B-FABP,FATTY ACID-BINDING PROTEIN 7,MAMMARY-DERIVED COMPND 6 GROWTH INHIBITOR RELATED; 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: FABP7, BLBP, FABPB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.C.WEI,K.ZHAO,L.YIN REVDAT 2 13-MAR-24 8IVF 1 JRNL REVDAT 1 28-FEB-24 8IVF 0 JRNL AUTH X.X.FANG,P.WEI,K.ZHAO,Z.C.SHENG,B.L.SONG,L.YIN,J.LUO JRNL TITL FATTY ACID-BINDING PROTEINS 3, 7, AND 8 BIND CHOLESTEROL AND JRNL TITL 2 FACILITATE ITS EGRESS FROM LYSOSOMES. JRNL REF J.CELL BIOL. V. 223 2024 JRNL REFN ESSN 1540-8140 JRNL PMID 38429999 JRNL DOI 10.1083/JCB.202211062 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 13896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1368 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 42.1400 - 5.6000 0.90 1235 132 0.2069 0.2560 REMARK 3 2 5.5900 - 4.4500 0.88 1192 126 0.1705 0.1833 REMARK 3 3 4.4400 - 3.8800 0.91 1209 130 0.1775 0.2184 REMARK 3 4 3.8800 - 3.5300 0.95 1285 140 0.1980 0.2230 REMARK 3 5 3.5300 - 3.2800 0.96 1333 145 0.2091 0.2821 REMARK 3 6 3.2800 - 3.0800 0.88 1171 121 0.2223 0.2412 REMARK 3 7 3.0800 - 2.9300 0.91 1235 127 0.2432 0.2954 REMARK 3 8 2.9300 - 2.8000 0.94 1280 155 0.2564 0.2970 REMARK 3 9 2.8000 - 2.6900 0.96 1286 141 0.2511 0.2814 REMARK 3 10 2.6900 - 2.6000 0.96 1302 151 0.2466 0.2745 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.480 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 : 0.027 2231 REMARK 3 ANGLE : 1.492 3032 REMARK 3 CHIRALITY : 0.112 350 REMARK 3 PLANARITY : 0.003 379 REMARK 3 DIHEDRAL : 23.186 317 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 8IVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300036484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13896 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 19.18 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 58.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.04300 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5 25% W/V PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.05500 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 1 CG SD CE REMARK 470 MET A 1 CG SD CE 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 ASP B 90 O HOH B 1101 1.94 REMARK 500 OE2 GLU A 102 O HOH A 1101 2.08 REMARK 500 N PHE A 28 O HOH A 1102 2.09 REMARK 500 NZ LYS B 49 O HOH B 1102 2.09 REMARK 500 O HOH B 1105 O HOH B 1135 2.11 REMARK 500 OG1 THR A 12 O HOH A 1103 2.11 REMARK 500 O HOH A 1139 O HOH A 1155 2.11 REMARK 500 O GLU A 70 O HOH A 1104 2.12 REMARK 500 OE2 GLU A 62 O HOH A 1105 2.12 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 ALA A 7 -177.03 -173.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IVF B 1 132 UNP O15540 FABP7_HUMAN 1 132 DBREF 8IVF A 1 132 UNP O15540 FABP7_HUMAN 1 132 SEQRES 1 B 132 MET VAL GLU ALA PHE CYS ALA THR TRP LYS LEU THR ASN SEQRES 2 B 132 SER GLN ASN PHE ASP GLU TYR MET LYS ALA LEU GLY VAL SEQRES 3 B 132 GLY PHE ALA THR ARG GLN VAL GLY ASN VAL THR LYS PRO SEQRES 4 B 132 THR VAL ILE ILE SER GLN GLU GLY ASP LYS VAL VAL ILE SEQRES 5 B 132 ARG THR LEU SER THR PHE LYS ASN THR GLU ILE SER PHE SEQRES 6 B 132 GLN LEU GLY GLU GLU PHE ASP GLU THR THR ALA ASP ASP SEQRES 7 B 132 ARG ASN CYS LYS SER VAL VAL SER LEU ASP GLY ASP LYS SEQRES 8 B 132 LEU VAL HIS ILE GLN LYS TRP ASP GLY LYS GLU THR ASN SEQRES 9 B 132 PHE VAL ARG GLU ILE LYS ASP GLY LYS MET VAL MET THR SEQRES 10 B 132 LEU THR PHE GLY ASP VAL VAL ALA VAL ARG HIS TYR GLU SEQRES 11 B 132 LYS ALA SEQRES 1 A 132 MET VAL GLU ALA PHE CYS ALA THR TRP LYS LEU THR ASN SEQRES 2 A 132 SER GLN ASN PHE ASP GLU TYR MET LYS ALA LEU GLY VAL SEQRES 3 A 132 GLY PHE ALA THR ARG GLN VAL GLY ASN VAL THR LYS PRO SEQRES 4 A 132 THR VAL ILE ILE SER GLN GLU GLY ASP LYS VAL VAL ILE SEQRES 5 A 132 ARG THR LEU SER THR PHE LYS ASN THR GLU ILE SER PHE SEQRES 6 A 132 GLN LEU GLY GLU GLU PHE ASP GLU THR THR ALA ASP ASP SEQRES 7 A 132 ARG ASN CYS LYS SER VAL VAL SER LEU ASP GLY ASP LYS SEQRES 8 A 132 LEU VAL HIS ILE GLN LYS TRP ASP GLY LYS GLU THR ASN SEQRES 9 A 132 PHE VAL ARG GLU ILE LYS ASP GLY LYS MET VAL MET THR SEQRES 10 A 132 LEU THR PHE GLY ASP VAL VAL ALA VAL ARG HIS TYR GLU SEQRES 11 A 132 LYS ALA HET HC3 B1001 29 HET HC3 A1001 29 HETNAM HC3 25-HYDROXYCHOLESTEROL HETSYN HC3 (3BETA)-CHOLEST-5-ENE-3,25-DIOL FORMUL 3 HC3 2(C27 H46 O2) FORMUL 5 HOH *106(H2 O) HELIX 1 AA1 VAL B 2 CYS B 6 5 5 HELIX 2 AA2 ASN B 16 GLY B 25 1 10 HELIX 3 AA3 GLY B 27 ASN B 35 1 9 HELIX 4 AA4 MET A 1 CYS A 6 5 6 HELIX 5 AA5 ASN A 16 GLY A 25 1 10 HELIX 6 AA6 GLY A 27 ASN A 35 1 9 SHEET 1 AA110 THR B 61 PHE B 65 0 SHEET 2 AA110 LYS B 49 LEU B 55 -1 N VAL B 50 O PHE B 65 SHEET 3 AA110 THR B 40 GLU B 46 -1 N THR B 40 O LEU B 55 SHEET 4 AA110 THR B 8 GLN B 15 -1 N TRP B 9 O VAL B 41 SHEET 5 AA110 VAL B 123 LYS B 131 -1 O VAL B 126 N GLN B 15 SHEET 6 AA110 LYS B 113 PHE B 120 -1 N LEU B 118 O ALA B 125 SHEET 7 AA110 LYS B 101 LYS B 110 -1 N LYS B 110 O LYS B 113 SHEET 8 AA110 LYS B 91 TRP B 98 -1 N LEU B 92 O ARG B 107 SHEET 9 AA110 ASN B 80 ASP B 88 -1 N ASP B 88 O LYS B 91 SHEET 10 AA110 PHE B 71 THR B 74 -1 N GLU B 73 O CYS B 81 SHEET 1 AA210 THR A 61 PHE A 65 0 SHEET 2 AA210 LYS A 49 LEU A 55 -1 N THR A 54 O THR A 61 SHEET 3 AA210 THR A 40 GLU A 46 -1 N ILE A 42 O ARG A 53 SHEET 4 AA210 ALA A 7 GLN A 15 -1 N TRP A 9 O VAL A 41 SHEET 5 AA210 VAL A 123 LYS A 131 -1 O HIS A 128 N THR A 12 SHEET 6 AA210 LYS A 113 PHE A 120 -1 N LEU A 118 O ALA A 125 SHEET 7 AA210 LYS A 101 LYS A 110 -1 N LYS A 110 O LYS A 113 SHEET 8 AA210 LYS A 91 TRP A 98 -1 N HIS A 94 O PHE A 105 SHEET 9 AA210 ASN A 80 ASP A 88 -1 N ASP A 88 O LYS A 91 SHEET 10 AA210 PHE A 71 THR A 74 -1 N PHE A 71 O SER A 83 CRYST1 34.700 54.110 67.240 90.00 92.34 90.00 P 1 21 1 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 0.028819 0.000000 0.001178 0.00000 SCALE2 0.000000 0.018481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014884 0.00000