HEADER LIPID BINDING PROTEIN 13-MAY-04 1T8V TITLE THE NMR STRUCTURE OF D34A I-FABP: IMPLICATIONS FOR THE DETERMINANTS OF TITLE 2 LIGAND BINDING STOICHIOMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: FATTY ACID-BINDING PROTEIN, INTESTINAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: I-FABP, D34A I-FABP, FABPI; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: FABP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FATTY ACID, STOICHIOMETRY, LIPID BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.OGBAY,D.P.CISTOLA REVDAT 3 27-OCT-21 1T8V 1 REMARK SEQADV REVDAT 2 24-FEB-09 1T8V 1 VERSN REVDAT 1 04-OCT-05 1T8V 0 JRNL AUTH B.OGBAY,D.P.CISTOLA JRNL TITL THE NMR STRUCTURE OF D34A I-FABP: IMPLICATIONS FOR THE JRNL TITL 2 DETERMINANTS OF LIGAND BINDING STOICHIOMETRY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.P.CISTOLA,B.OGBAY,G.T.DEKOSTER REMARK 1 TITL THE NMR STRUCTURE OF A STABLE AND COMPACT ALL-B-SHEET REMARK 1 TITL 2 VARIANT OF INTESTINAL FATTY ACID-BINDING PROTEIN REMARK 1 REF PROTEIN SCI. V. 13 1227 2004 REMARK 1 REFN ISSN 0961-8368 REMARK 1 DOI 10.1110/PS.03546204 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, ARIA 1.2 REMARK 3 AUTHORS : VARIAN ASSOCIATES (VNMR), LINGE, O'DONOGHUE, REMARK 3 NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 3471 NOE-DERIVED RESTRAINTS AND 80 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1T8V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022457. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 50MM KCL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 20 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 KCL, 0.5% NAN3, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C_ REMARK 210 AROMATIC_NOESY; 3D_15N-15N_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2001, CNS 1.1, ARIA 1.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS 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 HG13 VAL A 105 H THR A 116 1.17 REMARK 500 HD22 ASN A 11 HD2 LYS A 16 1.23 REMARK 500 HB VAL A 61 HZ PHE A 68 1.30 REMARK 500 HG2 LYS A 46 HG23 THR A 48 1.32 REMARK 500 HB2 LYS A 16 HD1 PHE A 17 1.32 REMARK 500 HG2 ARG A 10 HH21 ARG A 126 1.33 REMARK 500 H TYR A 14 HA3 GLY A 31 1.34 REMARK 500 H LEU A 89 HB2 ARG A 106 1.35 REMARK 500 H LEU A 78 HG23 VAL A 96 1.35 REMARK 500 OE1 GLU A 107 HZ3 LYS A 129 1.48 REMARK 500 O GLU A 15 H GLU A 19 1.52 REMARK 500 HZ1 LYS A 50 OD1 ASP A 59 1.55 REMARK 500 O TYR A 119 H GLY A 121 1.56 REMARK 500 HB THR A 39 O VAL A 49 1.58 REMARK 500 OE1 GLU A 77 HH12 ARG A 95 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 6 GLY A 80 N GLY A 80 CA -0.092 REMARK 500 7 GLY A 80 N GLY A 80 CA -0.097 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 1 ASP A 3 -50.56 -138.14 REMARK 500 1 VAL A 8 -60.99 -171.81 REMARK 500 1 ASP A 9 -166.94 -125.77 REMARK 500 1 ARG A 10 -173.14 -170.94 REMARK 500 1 LYS A 20 -43.92 -140.21 REMARK 500 1 ILE A 23 -71.46 65.38 REMARK 500 1 ASN A 24 -140.07 44.80 REMARK 500 1 ARG A 28 30.16 -87.46 REMARK 500 1 HIS A 33 39.41 169.57 REMARK 500 1 ALA A 34 139.61 -173.69 REMARK 500 1 ILE A 40 109.00 -164.27 REMARK 500 1 GLN A 42 -77.31 -175.99 REMARK 500 1 ASN A 45 82.15 -175.47 REMARK 500 1 PHE A 47 97.85 -163.45 REMARK 500 1 THR A 48 101.28 -168.32 REMARK 500 1 VAL A 49 103.98 -169.61 REMARK 500 1 LYS A 50 101.52 -168.05 REMARK 500 1 PHE A 55 -45.22 -146.68 REMARK 500 1 ILE A 58 126.18 -174.39 REMARK 500 1 VAL A 61 114.17 -168.41 REMARK 500 1 ALA A 73 51.71 -161.97 REMARK 500 1 ASP A 74 -140.43 -168.83 REMARK 500 1 THR A 76 117.02 -163.15 REMARK 500 1 GLU A 77 94.81 -163.82 REMARK 500 1 TRP A 82 105.43 -161.16 REMARK 500 1 ASN A 87 -25.99 165.22 REMARK 500 1 VAL A 90 101.97 -167.70 REMARK 500 1 ARG A 95 -174.38 -58.51 REMARK 500 1 ASN A 98 -67.14 -157.88 REMARK 500 1 LEU A 102 122.41 -172.35 REMARK 500 1 ILE A 103 121.82 -175.14 REMARK 500 1 ALA A 104 102.09 -169.35 REMARK 500 1 SER A 109 102.34 -169.27 REMARK 500 1 GLU A 112 131.48 -171.06 REMARK 500 1 TYR A 119 101.51 -171.90 REMARK 500 1 GLU A 120 -58.91 67.45 REMARK 500 1 VAL A 122 110.28 -163.43 REMARK 500 1 ARG A 126 111.30 -165.47 REMARK 500 1 LYS A 130 130.57 62.51 REMARK 500 2 ASP A 3 23.55 -165.32 REMARK 500 2 LYS A 7 114.87 -168.35 REMARK 500 2 VAL A 8 -63.61 -163.50 REMARK 500 2 LYS A 20 -47.20 -150.79 REMARK 500 2 MET A 21 -70.71 -47.39 REMARK 500 2 ILE A 23 -50.10 69.50 REMARK 500 2 ASN A 24 -141.09 44.56 REMARK 500 2 VAL A 26 -26.37 71.94 REMARK 500 2 LYS A 27 -92.69 47.78 REMARK 500 2 LYS A 29 95.25 -61.93 REMARK 500 2 ALA A 32 -96.09 -87.15 REMARK 500 REMARK 500 THIS ENTRY HAS 420 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 44 ASN A 45 1 149.38 REMARK 500 GLY A 80 THR A 81 1 148.80 REMARK 500 GLY A 80 THR A 81 2 147.16 REMARK 500 GLY A 44 ASN A 45 4 148.14 REMARK 500 GLY A 86 ASN A 87 5 148.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 106 0.11 SIDE CHAIN REMARK 500 2 ARG A 126 0.08 SIDE CHAIN REMARK 500 3 ARG A 106 0.10 SIDE CHAIN REMARK 500 5 ARG A 106 0.16 SIDE CHAIN REMARK 500 6 ARG A 106 0.09 SIDE CHAIN REMARK 500 9 ARG A 106 0.09 SIDE CHAIN REMARK 500 10 ARG A 106 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 THR A 5 10.48 REMARK 500 1 TRP A 6 10.29 REMARK 500 1 VAL A 8 10.49 REMARK 500 1 GLU A 12 -11.81 REMARK 500 1 GLY A 44 -15.56 REMARK 500 1 GLY A 80 -16.39 REMARK 500 1 VAL A 105 -10.37 REMARK 500 1 GLY A 110 -12.86 REMARK 500 2 GLU A 12 -10.30 REMARK 500 2 GLY A 44 -15.40 REMARK 500 2 THR A 79 -10.66 REMARK 500 2 GLY A 80 -15.46 REMARK 500 2 VAL A 105 -10.29 REMARK 500 2 GLY A 110 -12.11 REMARK 500 3 VAL A 8 11.89 REMARK 500 3 GLU A 12 -10.81 REMARK 500 3 GLY A 44 -14.29 REMARK 500 3 LYS A 46 -10.20 REMARK 500 3 THR A 79 -11.89 REMARK 500 3 GLY A 80 -14.03 REMARK 500 3 VAL A 105 -10.59 REMARK 500 3 GLY A 110 -12.63 REMARK 500 3 ILE A 127 -10.34 REMARK 500 4 LYS A 7 -11.49 REMARK 500 4 VAL A 8 10.84 REMARK 500 4 GLU A 12 -10.09 REMARK 500 4 GLU A 19 10.28 REMARK 500 4 GLY A 44 -16.07 REMARK 500 4 THR A 79 -13.78 REMARK 500 4 MET A 84 -10.82 REMARK 500 4 GLY A 110 -13.47 REMARK 500 4 PHE A 128 13.42 REMARK 500 5 THR A 5 10.13 REMARK 500 5 TRP A 6 11.87 REMARK 500 5 GLU A 12 -12.81 REMARK 500 5 GLY A 44 -14.53 REMARK 500 5 LYS A 46 -13.55 REMARK 500 5 THR A 79 -13.00 REMARK 500 5 GLY A 86 -14.07 REMARK 500 5 ARG A 106 -10.60 REMARK 500 5 GLY A 110 -12.21 REMARK 500 5 LYS A 125 10.37 REMARK 500 5 PHE A 128 10.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AEL RELATED DB: PDB REMARK 900 NMR STRUCTURE OF APO INTESTINAL FATTY ACID-BINDING PROTEIN REMARK 900 RELATED ID: 1IFC RELATED DB: PDB REMARK 900 INTESTINAL FATTY ACID BINDING PROTEIN REMARK 900 RELATED ID: 1IFB RELATED DB: PDB REMARK 900 INTESTINAL FATTY ACID BINDING PROTEIN (APO FORM 1) (I-FABP) REMARK 900 RELATED ID: 2IFB RELATED DB: PDB REMARK 900 INTESTINAL FATTY ACID BINDING PROTEIN (HOLO FORM) (I-FABP) DBREF 1T8V A 1 131 UNP P02693 FABPI_RAT 1 131 SEQADV 1T8V ALA A 34 UNP P02693 ASP 34 ENGINEERED MUTATION SEQRES 1 A 131 ALA PHE ASP GLY THR TRP LYS VAL ASP ARG ASN GLU ASN SEQRES 2 A 131 TYR GLU LYS PHE MET GLU LYS MET GLY ILE ASN VAL VAL SEQRES 3 A 131 LYS ARG LYS LEU GLY ALA HIS ALA ASN LEU LYS LEU THR SEQRES 4 A 131 ILE THR GLN GLU GLY ASN LYS PHE THR VAL LYS GLU SER SEQRES 5 A 131 SER ASN PHE ARG ASN ILE ASP VAL VAL PHE GLU LEU GLY SEQRES 6 A 131 VAL ASP PHE ALA TYR SER LEU ALA ASP GLY THR GLU LEU SEQRES 7 A 131 THR GLY THR TRP THR MET GLU GLY ASN LYS LEU VAL GLY SEQRES 8 A 131 LYS PHE LYS ARG VAL ASP ASN GLY LYS GLU LEU ILE ALA SEQRES 9 A 131 VAL ARG GLU ILE SER GLY ASN GLU LEU ILE GLN THR TYR SEQRES 10 A 131 THR TYR GLU GLY VAL GLU ALA LYS ARG ILE PHE LYS LYS SEQRES 11 A 131 GLU HELIX 1 1 GLU A 15 MET A 21 1 7 SHEET 1 A 5 GLY A 4 GLU A 12 0 SHEET 2 A 5 LYS A 37 GLN A 42 -1 N LEU A 38 O TRP A 6 SHEET 3 A 5 LYS A 46 SER A 53 -1 N LYS A 50 O THR A 39 SHEET 4 A 5 ASN A 57 GLU A 63 -1 N VAL A 60 O VAL A 49 SHEET 5 A 5 VAL A 66 SER A 71 -1 SHEET 1 B 5 LEU A 78 GLU A 85 0 SHEET 2 B 5 LYS A 88 PHE A 93 -1 N VAL A 90 O THR A 83 SHEET 3 B 5 GLU A 101 SER A 109 -1 N ALA A 104 O GLY A 91 SHEET 4 B 5 GLU A 112 TYR A 119 -1 N THR A 116 O VAL A 105 SHEET 5 B 5 VAL A 122 LYS A 129 -1 N ARG A 126 O GLN A 115 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1