HEADER LIPID BINDING PROTEIN 30-JUL-00 1FH1 TITLE BACKBONE FOLD OF NODF COMPND MOL_ID: 1; COMPND 2 MOLECULE: NODULATION PROTEIN F; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NODF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOBIUM LEGUMINOSARUM; SOURCE 3 ORGANISM_TAXID: 384; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PMP2301 KEYWDS ROOT NODULATION FACTOR, PROTEIN BACKBONE FOLD, LIPID KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR AUTHOR C.A.FOWLER,F.TIAN,H.M.AL-HASHIMI,J.H.PRESTEGARD REVDAT 2 24-FEB-09 1FH1 1 VERSN REVDAT 1 17-JAN-01 1FH1 0 JRNL AUTH C.A.FOWLER,F.TIAN,H.M.AL-HASHIMI,J.H.PRESTEGARD JRNL TITL RAPID DETERMINATION OF PROTEIN FOLDS USING JRNL TITL 2 RESIDUAL DIPOLAR COUPLINGS. JRNL REF J.MOL.BIOL. V. 304 447 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11090286 JRNL DOI 10.1006/JMBI.2000.4199 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.GHOSE,O.GEIGER,J.H.PRESTEGARD REMARK 1 TITL NMR INVESTIGATIONS OF THE STRUCTURAL PROPERTIES OF REMARK 1 TITL 2 THE NODULATION PROTEIN, NODF, FROM RHIZOBIUM REMARK 1 TITL 3 LEGUMINOSARUM AND ITS HOMOLOGY WITH ESCHERICIA REMARK 1 TITL 4 COLI ACYL CARRIER PROTEIN REMARK 1 REF FEBS LETT. V. 388 66 1996 REMARK 1 REFN ISSN 0014-5793 REMARK 1 DOI 10.1016/0014-5793(96)00512-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : POSE REMARK 3 AUTHORS : FOWLER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SECONDARY STRUCTURAL ELEMENTS (3 REMARK 3 HELICES) WERE IDENTIFIED. THESE WERE SPLIT INTO SMALLER REMARK 3 FRAGMENTS AND INDIVIDUAL FRAGMENTS WERE ORIENTED USING REMARK 3 RESIDUAL DIPOLAR COUPLING DATA AND THE PROGRAM ORDERTEN_SVD REMARK 3 (LOSONCZI, ET AL., J. MAGN. RES., 138, 334-342, 1999). THE REMARK 3 FRAGMENTS WERE REASSEMBLED AND THEN POSITIONED SPATIALLY BY REMARK 3 TRANSLATION USING A LIMITED SET OF NOES TO PRODUCE A BACKBONE REMARK 3 FOLD OF THE NODF PROTEIN. THERE ARE N-CA-C ANGLE ERRORS (AS REMARK 3 COMPARED TO THE STANDARD DICTIONARY) AT RESIDUES 13 AND 80. REMARK 3 RESIDUE 80 LIES SOMEWHAT OUTSIDE ALLOWED RAMACHANDRAN SPACE. REMARK 3 THESE SITES ARE POSITIONS WHERE ORIENTED HELICAL FRAGMENTS REMARK 3 WERE REASSEMBLED INTO COMPLETE HELICES DURING DETERMINATION OF REMARK 3 OF THE BACKBONE FOLD AND ANY SMALLER LOCAL DISTORTIONS FROM REMARK 3 IDEALITY ARE EXPECTED TO CONCENTRATE HERE. THE STRUCTURE REMARK 3 PRESENTED HERE CONTAINS ONLY COORDINATES FOR BACKBONE ATOMS REMARK 3 INVOLVED IN SECONDARY STRUCTURE. THE STRUCTURE IS THE AVERAGE REMARK 3 OF AN ENSEMBLE WITH A HEAVY ATOM RMSD OF 2.4 ANGSTROMS. CB REMARK 3 POSITIONS COME FROM POLYALANINE HELICES USED TO MODEL THE REMARK 3 BACKBONE. REMARK 4 REMARK 4 1FH1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-00. REMARK 100 THE RCSB ID CODE IS RCSB011579. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.1; 6.1 REMARK 210 IONIC STRENGTH : 0; 0 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.5 MM NODF ISOTROPIC U-15N, REMARK 210 13C 200 MM PHOSPHATE BUFFER, REMARK 210 PH 6.1; 1.0 MM NODF ALIGNED U- REMARK 210 15N,13C 200 MM PHOSPHATE REMARK 210 BUFFER, PH 6.1 20 MG/ML PF1 REMARK 210 BACTERIOPHAGE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 98, ORDERTEN_SVD, POSE REMARK 210 METHOD USED : OTHER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: ASSIGNMENTS WERE MADE USING DOUBLE AND TRIPLE-RESONANCE REMARK 210 NMR SPECTROSCOPY. DIPOLAR COUPLINGS WERE MEASURED AND USED TO REMARK 210 PRODUCE THE PROTEIN BACKBONE FOLD. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 GLN A 4 REMARK 465 LYS A 18 REMARK 465 ALA A 19 REMARK 465 GLU A 20 REMARK 465 ASN A 21 REMARK 465 GLY A 22 REMARK 465 GLU A 23 REMARK 465 ARG A 24 REMARK 465 THR A 25 REMARK 465 SER A 26 REMARK 465 VAL A 27 REMARK 465 ALA A 28 REMARK 465 LEU A 29 REMARK 465 GLY A 30 REMARK 465 GLU A 31 REMARK 465 ILE A 32 REMARK 465 THR A 33 REMARK 465 THR A 34 REMARK 465 ASP A 35 REMARK 465 THR A 36 REMARK 465 GLU A 37 REMARK 465 LEU A 38 REMARK 465 THR A 39 REMARK 465 SER A 40 REMARK 465 LEU A 41 REMARK 465 GLY A 42 REMARK 465 ILE A 43 REMARK 465 ASP A 44 REMARK 465 SER A 45 REMARK 465 TYR A 59 REMARK 465 GLY A 60 REMARK 465 ILE A 61 REMARK 465 LYS A 62 REMARK 465 ILE A 63 REMARK 465 GLU A 64 REMARK 465 MET A 65 REMARK 465 ASN A 66 REMARK 465 THR A 67 REMARK 465 ALA A 68 REMARK 465 ASP A 69 REMARK 465 ALA A 70 REMARK 465 TRP A 71 REMARK 465 SER A 72 REMARK 465 ASN A 73 REMARK 465 LEU A 74 REMARK 465 ASN A 75 REMARK 465 LEU A 87 REMARK 465 LEU A 88 REMARK 465 THR A 89 REMARK 465 LYS A 90 REMARK 465 GLU A 91 REMARK 465 VAL A 92 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 LEU A 5 CG CD1 CD2 REMARK 470 THR A 6 OG1 CG2 REMARK 470 LEU A 7 CG CD1 CD2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 ILE A 9 CG1 CG2 CD1 REMARK 470 ILE A 10 CG1 CG2 CD1 REMARK 470 SER A 11 OG REMARK 470 ILE A 13 CG1 CG2 CD1 REMARK 470 ASN A 14 CG OD1 ND2 REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 LEU A 16 CG CD1 CD2 REMARK 470 VAL A 17 CG1 CG2 REMARK 470 LEU A 46 CG CD1 CD2 REMARK 470 LEU A 48 CG CD1 CD2 REMARK 470 ASP A 50 CG OD1 OD2 REMARK 470 VAL A 51 CG1 CG2 REMARK 470 LEU A 52 CG CD1 CD2 REMARK 470 TRP A 53 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 53 CZ3 CH2 REMARK 470 ASP A 54 CG OD1 OD2 REMARK 470 LEU A 55 CG CD1 CD2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLN A 57 CG CD OE1 NE2 REMARK 470 LEU A 58 CG CD1 CD2 REMARK 470 ASN A 76 CG OD1 ND2 REMARK 470 ILE A 77 CG1 CG2 CD1 REMARK 470 ASP A 79 CG OD1 OD2 REMARK 470 VAL A 80 CG1 CG2 REMARK 470 VAL A 81 CG1 CG2 REMARK 470 GLU A 82 CG CD OE1 OE2 REMARK 470 VAL A 84 CG1 CG2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 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 O LEU A 7 CB ILE A 10 1.11 REMARK 500 O VAL A 81 N ALA A 83 1.74 REMARK 500 O GLU A 8 N SER A 11 1.88 REMARK 500 O LEU A 7 CA ILE A 10 1.95 REMARK 500 O LEU A 7 N ILE A 10 2.13 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 ILE A 9 N - CA - C ANGL. DEV. = -25.9 DEGREES REMARK 500 ILE A 13 N - CA - CB ANGL. DEV. = -23.0 DEGREES REMARK 500 ILE A 13 N - CA - C ANGL. DEV. = 43.9 DEGREES REMARK 500 ASP A 50 N - CA - C ANGL. DEV. = 29.4 DEGREES REMARK 500 TRP A 53 N - CA - CB ANGL. DEV. = 20.1 DEGREES REMARK 500 VAL A 80 N - CA - CB ANGL. DEV. = -52.0 DEGREES REMARK 500 VAL A 80 N - CA - C ANGL. DEV. = 43.5 DEGREES REMARK 500 GLU A 82 N - CA - CB ANGL. DEV. = -19.1 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 ASP A 50 -89.30 -99.36 REMARK 500 TRP A 53 -80.70 -44.84 REMARK 500 VAL A 80 7.41 145.50 REMARK 500 GLU A 82 -24.02 -22.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 1FH1 A 1 92 UNP P04685 NODF_RHILV 1 92 SEQRES 1 A 92 MET ALA ASP GLN LEU THR LEU GLU ILE ILE SER ALA ILE SEQRES 2 A 92 ASN LYS LEU VAL LYS ALA GLU ASN GLY GLU ARG THR SER SEQRES 3 A 92 VAL ALA LEU GLY GLU ILE THR THR ASP THR GLU LEU THR SEQRES 4 A 92 SER LEU GLY ILE ASP SER LEU GLY LEU ALA ASP VAL LEU SEQRES 5 A 92 TRP ASP LEU GLU GLN LEU TYR GLY ILE LYS ILE GLU MET SEQRES 6 A 92 ASN THR ALA ASP ALA TRP SER ASN LEU ASN ASN ILE GLY SEQRES 7 A 92 ASP VAL VAL GLU ALA VAL ARG GLY LEU LEU THR LYS GLU SEQRES 8 A 92 VAL HELIX 1 1 LEU A 5 VAL A 17 1 13 HELIX 2 2 ASP A 50 LEU A 58 1 9 HELIX 3 3 VAL A 81 GLY A 86 1 6 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 MASTER 238 0 0 3 0 0 0 6 0 0 0 8 END