HEADER BINDING PROTEIN 20-JUL-92 1MDC TITLE CRYSTALLIZATION, STRUCTURE DETERMINATION AND LEAST-SQUARES REFINEMENT TITLE 2 TO 1.75 ANGSTROMS RESOLUTION OF THE FATTY-ACID-BINDING PROTEIN TITLE 3 ISOLATED FROM MANDUCA SEXTA L COMPND MOL_ID: 1; COMPND 2 MOLECULE: INSECT FATTY ACID BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MANDUCA SEXTA; SOURCE 3 ORGANISM_COMMON: TOBACCO HORNWORM; SOURCE 4 ORGANISM_TAXID: 7130 KEYWDS BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BENNING,H.M.HOLDEN REVDAT 7 06-NOV-24 1MDC 1 REMARK SEQADV LINK REVDAT 6 29-NOV-17 1MDC 1 HELIX REVDAT 5 13-JUL-11 1MDC 1 VERSN REVDAT 4 24-FEB-09 1MDC 1 VERSN REVDAT 3 01-APR-03 1MDC 1 JRNL REVDAT 2 30-APR-94 1MDC 3 HET FORMUL HETATM CONECT REVDAT 1 31-JAN-94 1MDC 0 JRNL AUTH M.M.BENNING,A.F.SMITH,M.A.WELLS,H.M.HOLDEN JRNL TITL CRYSTALLIZATION, STRUCTURE DETERMINATION AND LEAST-SQUARES JRNL TITL 2 REFINEMENT TO 1.75 A RESOLUTION OF THE FATTY-ACID-BINDING JRNL TITL 3 PROTEIN ISOLATED FROM MANDUCA SEXTA L. JRNL REF J.MOL.BIOL. V. 228 208 1992 JRNL REFN ISSN 0022-2836 JRNL PMID 1447782 JRNL DOI 10.1016/0022-2836(92)90501-A REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10674 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 984 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.016 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.680 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 35.40000 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 13 CD GLU A 13 OE2 -0.072 REMARK 500 GLU A 68 CD GLU A 68 OE2 -0.066 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 16 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 26 CB - CG - OD1 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 77 CB - CG - OD1 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP A 77 CB - CG - OD2 ANGL. DEV. = 9.0 DEGREES REMARK 500 ASP A 86 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 97 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 SER A 118 N - CA - CB ANGL. DEV. = -10.1 DEGREES 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 ASN A 14 19.42 58.83 REMARK 500 ALA A 75 57.16 -105.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS REMARK 700 ACTUALLY A TEN-STRANDED BETA-BARREL. THIS IS REPRESENTED REMARK 700 BY AN ELEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST REMARK 700 STRANDS ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 133 DBREF 1MDC A 1 131 UNP P31417 FABP2_MANSE 1 131 SEQADV 1MDC ASN A 50 UNP P31417 ILE 50 CONFLICT SEQADV 1MDC GLY A 55 UNP P31417 ILE 55 CONFLICT SEQADV 1MDC ALA A 58 UNP P31417 GLU 58 CONFLICT SEQADV 1MDC LYS A 59 UNP P31417 ARG 59 CONFLICT SEQADV 1MDC ASP A 77 UNP P31417 GLU 77 CONFLICT SEQRES 1 A 132 ACE SER TYR LEU GLY LYS VAL TYR SER LEU VAL LYS GLN SEQRES 2 A 132 GLU ASN PHE ASP GLY PHE LEU LYS SER ALA GLY LEU SER SEQRES 3 A 132 ASP ASP LYS ILE GLN ALA LEU VAL SER ASP LYS PRO THR SEQRES 4 A 132 GLN LYS MET GLU ALA ASN GLY ASP SER TYR SER ASN THR SEQRES 5 A 132 SER THR GLY GLY GLY GLY ALA LYS THR VAL SER PHE LYS SEQRES 6 A 132 SER GLY VAL GLU PHE ASP ASP VAL ILE GLY ALA GLY ASP SEQRES 7 A 132 SER VAL LYS SER MET TYR THR VAL ASP GLY ASN VAL VAL SEQRES 8 A 132 THR HIS VAL VAL LYS GLY ASP ALA GLY VAL ALA THR PHE SEQRES 9 A 132 LYS LYS GLU TYR ASN GLY ASP ASP LEU VAL VAL THR ILE SEQRES 10 A 132 THR SER SER ASN TRP ASP GLY VAL ALA ARG ARG TYR TYR SEQRES 11 A 132 LYS ALA HET ACE A 0 3 HET SO4 A 200 5 HET PLM A 133 18 HETNAM ACE ACETYL GROUP HETNAM SO4 SULFATE ION HETNAM PLM PALMITIC ACID FORMUL 1 ACE C2 H4 O FORMUL 2 SO4 O4 S 2- FORMUL 3 PLM C16 H32 O2 FORMUL 4 HOH *70(H2 O) HELIX 1 PHE A 15 ALA A 22 1 8 HELIX 2 ASP A 26 SER A 34 1 9 SHEET 1 S111 TYR A 7 GLU A 13 0 SHEET 2 S111 PRO A 37 ALA A 43 -1 SHEET 3 S111 TYR A 48 THR A 53 -1 SHEET 4 S111 ALA A 58 PHE A 63 -1 SHEET 5 S111 GLU A 68 VAL A 72 -1 SHEET 6 S111 ASP A 77 VAL A 85 -1 SHEET 7 S111 VAL A 90 LYS A 95 -1 SHEET 8 S111 VAL A 100 TYR A 107 -1 SHEET 9 S111 LEU A 112 THR A 117 -1 SHEET 10 S111 VAL A 124 ALA A 131 -1 SHEET 11 S111 TYR A 7 GLU A 13 -1 LINK C ACE A 0 N SER A 1 1555 1555 1.35 SITE 1 AC1 6 GLN A 39 ASN A 50 TYR A 83 HIS A 92 SITE 2 AC1 6 LYS A 105 PLM A 133 SITE 1 AC2 6 GLN A 39 GLY A 99 VAL A 114 ARG A 127 SITE 2 AC2 6 TYR A 129 SO4 A 200 CRYST1 27.500 70.800 28.500 90.00 90.50 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 0.036364 0.000000 0.000317 0.00000 SCALE2 0.000000 0.014124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035089 0.00000 HETATM 1 C ACE A 0 11.123 38.153 4.625 1.00 8.15 C HETATM 2 O ACE A 0 12.127 38.219 5.466 1.00 12.83 O HETATM 3 CH3 ACE A 0 11.361 38.211 3.115 1.00 12.60 C