HEADER LIPID BINDING PROTEIN 08-SEP-17 6AYL TITLE HUMAN ADIPOCYTE LIPID-BINDING PROTEIN FABP4 IN COMPLEX WITH TITLE 2 FLUORESCEIN 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,AFABP,FATTY ACID-BINDING PROTEIN 4; COMPND 6 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: FABP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.POZHARSKI REVDAT 2 04-OCT-23 6AYL 1 REMARK REVDAT 1 12-SEP-18 6AYL 0 JRNL AUTH E.POZHARSKI,F.S.ST JOHN JRNL TITL TO BE PUBLISHED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 11169 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 548 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.04 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.46 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2268 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2380 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2161 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.72 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 107 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 985 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -17.48270 REMARK 3 B22 (A**2) : 2.20340 REMARK 3 B33 (A**2) : 15.27930 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.320 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.169 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.141 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.162 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.138 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1086 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1481 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 363 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 22 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 225 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1086 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 147 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1224 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.16 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.17 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6AYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 75.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.20400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: 3RZY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 16.59500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.49500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.49500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.50500 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: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6600 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 GLN A -7 REMARK 465 GLN A -6 REMARK 465 MET A -5 REMARK 465 GLY A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 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 LYS A 9 CG CD CE NZ REMARK 470 GLU A 14 CD OE1 OE2 REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 PHE A 57 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 76 CG OD1 OD2 REMARK 470 ASP A 77 CG OD1 OD2 REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 ASP A 98 CG OD1 OD2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 LYS A 112 CE NZ REMARK 470 LYS A 120 CG CD CE NZ 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 LYS A 37 76.64 -118.23 REMARK 500 ALA A 75 45.10 -79.25 REMARK 500 ASP A 98 -119.21 60.09 REMARK 500 ASP A 110 -125.65 55.12 REMARK 500 ASP A 110 -127.02 57.22 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 FLU A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLU A 202 DBREF 6AYL A 0 131 UNP P15090 FABP4_HUMAN 1 132 SEQADV 6AYL GLN A -7 UNP P15090 EXPRESSION TAG SEQADV 6AYL GLN A -6 UNP P15090 EXPRESSION TAG SEQADV 6AYL MET A -5 UNP P15090 EXPRESSION TAG SEQADV 6AYL GLY A -4 UNP P15090 EXPRESSION TAG SEQADV 6AYL ARG A -3 UNP P15090 EXPRESSION TAG SEQADV 6AYL GLY A -2 UNP P15090 EXPRESSION TAG SEQADV 6AYL SER A -1 UNP P15090 EXPRESSION TAG SEQRES 1 A 139 GLN GLN MET GLY ARG GLY SER MET CYS ASP ALA PHE VAL SEQRES 2 A 139 GLY THR TRP LYS LEU VAL SER SER GLU ASN PHE ASP ASP SEQRES 3 A 139 TYR MET LYS GLU VAL GLY VAL GLY PHE ALA THR ARG LYS SEQRES 4 A 139 VAL ALA GLY MET ALA LYS PRO ASN MET ILE ILE SER VAL SEQRES 5 A 139 ASN GLY ASP VAL ILE THR ILE LYS SER GLU SER THR PHE SEQRES 6 A 139 LYS ASN THR GLU ILE SER PHE ILE LEU GLY GLN GLU PHE SEQRES 7 A 139 ASP GLU VAL THR ALA ASP ASP ARG LYS VAL LYS SER THR SEQRES 8 A 139 ILE THR LEU ASP GLY GLY VAL LEU VAL HIS VAL GLN LYS SEQRES 9 A 139 TRP ASP GLY LYS SER THR THR ILE LYS ARG LYS ARG GLU SEQRES 10 A 139 ASP ASP LYS LEU VAL VAL GLU CYS VAL MET LYS GLY VAL SEQRES 11 A 139 THR SER THR ARG VAL TYR GLU ARG ALA HET FLU A 201 25 HET FLU A 202 25 HETNAM FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID HETSYN FLU FLUORESCEIN FORMUL 2 FLU 2(C20 H12 O5) FORMUL 4 HOH *51(H2 O) HELIX 1 AA1 SER A -1 PHE A 4 5 6 HELIX 2 AA2 ASN A 15 GLY A 24 1 10 HELIX 3 AA3 GLY A 26 ALA A 36 1 11 SHEET 1 AA110 ASN A 59 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 MET A 40 SHEET 5 AA110 VAL A 122 ARG A 130 -1 O VAL A 127 N VAL A 11 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 105 O GLU A 116 SHEET 8 AA110 VAL A 90 TRP A 97 -1 N HIS A 93 O ILE A 104 SHEET 9 AA110 VAL A 80 ASP A 87 -1 N ASP A 87 O VAL A 90 SHEET 10 AA110 PHE A 70 GLU A 72 -1 N PHE A 70 O SER A 82 SITE 1 AC1 15 PHE A 16 ALA A 36 PRO A 38 MET A 40 SITE 2 AC1 15 SER A 53 THR A 60 ILE A 62 ILE A 104 SITE 3 AC1 15 ARG A 106 CYS A 117 ARG A 126 TYR A 128 SITE 4 AC1 15 FLU A 202 HOH A 303 HOH A 304 SITE 1 AC2 11 VAL A 25 ALA A 33 LYS A 58 THR A 60 SITE 2 AC2 11 GLU A 72 THR A 74 ALA A 75 ARG A 78 SITE 3 AC2 11 FLU A 201 HOH A 306 HOH A 309 CRYST1 33.190 53.010 74.990 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 0.030130 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013335 0.00000