HEADER LIPID BINDING PROTEIN 04-DEC-02 1O8V TITLE THE CRYSTAL STRUCTURE OF ECHINOCOCCUS GRANULOSUS FATTY-ACID-BINDING TITLE 2 PROTEIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID BINDING PROTEIN HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FATTY ACID BINDING PROTEIN 1, FABP1, DF1, EGDF1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ACETYLATED AMINO TERMINUS, MODIFIED CYSTEINE A 63 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ECHINOCOCCUS GRANULOSUS; SOURCE 3 ORGANISM_TAXID: 6210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET-5A KEYWDS LIPID BINDING PROTEIN, FATTY-ACID-BINDING PROTEIN, ECHINOCOCCUS KEYWDS 2 GRANULOSUS, HYDATID DISEASE, FATTY-ACID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR E.JAKOBSSON,G.ALVITE,T.BERGFORS,A.ESTEVES,G.J.KLEYWEGT REVDAT 4 13-DEC-23 1O8V 1 REMARK REVDAT 3 09-OCT-19 1O8V 1 REMARK LINK REVDAT 2 24-FEB-09 1O8V 1 VERSN REVDAT 1 19-JUN-03 1O8V 0 JRNL AUTH E.JAKOBSSON,G.ALVITE,T.BERGFORS,A.ESTEVES,G.J.KLEYWEGT JRNL TITL THE CRYSTAL STRUCTURE OF ECHINOCOCCUS GRANULOSUS JRNL TITL 2 FATTY-ACID-BINDING PROTEIN 1 JRNL REF BIOCHIM.BIOPHYS.ACTA V.1649 40 2003 JRNL REFN ISSN 0006-3002 JRNL PMID 12818189 JRNL DOI 10.1016/S1570-9639(03)00151-1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15620 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1575 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1114 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1650 REMARK 3 BIN FREE R VALUE SET COUNT : 134 REMARK 3 BIN FREE R VALUE : 0.2160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1057 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : -0.90000 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.171 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1092 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1029 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1456 ; 1.420 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2416 ; 0.778 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 133 ; 6.021 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 165 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1161 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 204 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 158 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1185 ; 0.258 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 712 ; 0.077 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 87 ; 0.113 ; 0.200 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): 3 ; 0.132 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.349 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.137 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 THE LAST REFINEMENT ROUND WAS DONE AGAINST ALL DATA, REMARK 3 RFREE VALUES ARE THE LAST RECORDED REMARK 4 REMARK 4 1O8V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1290011828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0038 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : CYLINDRICAL GRAZING INCIDENCE REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15644 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.230 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.0000 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) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 14.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PMP CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) MMEPEG 5000, 0.1 M TRIS REMARK 280 -HCL,PH 8.6,0.1 M NAAC., PH 8.60 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 27.41700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 MEMBER OF THE FABP/P2/CRBP/CRABP FAMILY OF REMARK 400 TRANSPORTERS. 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 99 -11.89 87.79 REMARK 500 ASP A 121 -128.64 48.75 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 PLM A1136 DBREF 1O8V A 0 0 PDB 1O8V 1O8V 0 0 DBREF 1O8V A 1 133 UNP Q02970 FABP_ECHGR 1 133 SEQRES 1 A 134 ACE MET GLU ALA PHE LEU GLY THR TRP LYS MET GLU LYS SEQRES 2 A 134 SER GLU GLY PHE ASP LYS ILE MET GLU ARG LEU GLY VAL SEQRES 3 A 134 ASP PHE VAL THR ARG LYS MET GLY ASN LEU VAL LYS PRO SEQRES 4 A 134 ASN LEU ILE VAL THR ASP LEU GLY GLY GLY LYS TYR LYS SEQRES 5 A 134 MET ARG SER GLU SER THR PHE LYS THR THR GLU CSO SER SEQRES 6 A 134 PHE LYS LEU GLY GLU LYS PHE LYS GLU VAL THR PRO ASP SEQRES 7 A 134 SER ARG GLU VAL ALA SER LEU ILE THR VAL GLU ASN GLY SEQRES 8 A 134 VAL MET LYS HIS GLU GLN ASP ASP LYS THR LYS VAL THR SEQRES 9 A 134 TYR ILE GLU ARG VAL VAL GLU GLY ASN GLU LEU LYS ALA SEQRES 10 A 134 THR VAL LYS VAL ASP GLU VAL VAL CYS VAL ARG THR TYR SEQRES 11 A 134 SER LYS VAL ALA MODRES 1O8V CSO A 63 CYS S-HYDROXYCYSTEINE HET ACE A 0 3 HET CSO A 63 7 HET PLM A1136 18 HETNAM ACE ACETYL GROUP HETNAM CSO S-HYDROXYCYSTEINE HETNAM PLM PALMITIC ACID FORMUL 1 ACE C2 H4 O FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 PLM C16 H32 O2 FORMUL 3 HOH *143(H2 O) HELIX 1 1 GLU A 2 PHE A 4 5 3 HELIX 2 2 PHE A 16 LEU A 23 1 8 HELIX 3 3 PHE A 27 LEU A 35 1 9 SHEET 1 AA10 THR A 60 SER A 64 0 SHEET 2 AA10 LYS A 49 SER A 56 -1 O SER A 54 N THR A 61 SHEET 3 AA10 VAL A 36 LEU A 45 -1 O ASN A 39 N GLU A 55 SHEET 4 AA10 THR A 7 GLU A 14 -1 O TRP A 8 N LEU A 40 SHEET 5 AA10 VAL A 123 SER A 130 -1 O VAL A 126 N GLU A 14 SHEET 6 AA10 GLU A 113 VAL A 120 -1 O LEU A 114 N TYR A 129 SHEET 7 AA10 LYS A 101 GLU A 110 -1 O TYR A 104 N LYS A 119 SHEET 8 AA10 VAL A 91 ASP A 98 -1 O MET A 92 N ARG A 107 SHEET 9 AA10 ALA A 82 GLU A 88 -1 O ALA A 82 N ASP A 97 SHEET 10 AA10 GLU A 69 THR A 75 -1 O PHE A 71 N SER A 83 LINK C ACE A 0 N MET A 1 1555 1555 1.35 LINK C GLU A 62 N CSO A 63 1555 1555 1.32 LINK C CSO A 63 N SER A 64 1555 1555 1.33 SITE 1 AC1 13 PHE A 16 MET A 20 GLY A 33 VAL A 36 SITE 2 AC1 13 PRO A 76 ASP A 77 ARG A 79 GLN A 96 SITE 3 AC1 13 ARG A 107 ARG A 127 TYR A 129 HOH A2142 SITE 4 AC1 13 HOH A2143 CRYST1 28.714 54.834 38.691 90.00 100.34 90.00 P 1 21 1 2 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 0.034826 0.000000 0.006354 0.00000 SCALE2 0.000000 0.018237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026272 0.00000 HETATM 1 C ACE A 0 4.279 14.829 14.190 1.00 19.08 C HETATM 2 O ACE A 0 3.706 14.098 15.038 1.00 20.62 O HETATM 3 CH3 ACE A 0 3.827 16.236 14.001 1.00 20.22 C