PDB Short entry for 1AXJ HEADER BINDING PROTEIN 16-OCT-97 1AXJ TITLE FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS (MIYAZAKI F), NMR, 20 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: FMN-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'; SOURCE 3 ORGANISM_TAXID: 883; SOURCE 4 STRAIN: MIYAZAKI F; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMKBT-100 KEYWDS FMN-BINDING PROTEIN, BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.LIEPINSH,G.OTTING REVDAT 3 16-FEB-22 1AXJ 1 REMARK REVDAT 2 24-FEB-09 1AXJ 1 VERSN REVDAT 1 14-JAN-98 1AXJ 0 JRNL AUTH E.LIEPINSH,M.KITAMURA,T.MURAKAMI,T.NAKAYA,G.OTTING JRNL TITL PATHWAY OF CHYMOTRYPSIN EVOLUTION SUGGESTED BY THE STRUCTURE JRNL TITL 2 OF THE FMN-BINDING PROTEIN FROM DESULFOVIBRIO VULGARIS JRNL TITL 3 (MIYAZAKI F) JRNL REF NAT.STRUCT.BIOL. V. 4 975 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9406543 JRNL DOI 10.1038/NSB1297-975 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DIANA REMARK 3 AUTHORS : WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. OPAL (LUGINBUHL ET AL.) ALSO WAS USED. REMARK 4 REMARK 4 1AXJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171377. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 309 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; NOESY-15N-HSQC; NOESY-13C REMARK 210 -HSQC; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DIANA, OPAL REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 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 1 ARG A 92 CD - NE - CZ ANGL. DEV. = 10.3 DEGREES REMARK 500 3 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 60 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 92 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 17 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 19 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 20 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.1 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 1 GLU A 23 -61.68 -164.16 REMARK 500 1 MET A 51 71.41 -107.88 REMARK 500 1 VAL A 116 -54.99 -127.50 REMARK 500 1 THR A 121 -81.04 -134.83 REMARK 500 2 GLU A 23 -48.86 -161.42 REMARK 500 2 ASP A 24 40.63 -78.44 REMARK 500 2 ARG A 76 -78.63 -91.81 REMARK 500 2 PHE A 104 -179.00 -61.02 REMARK 500 2 VAL A 116 -54.77 -130.15 REMARK 500 2 THR A 121 -81.91 -135.37 REMARK 500 3 GLU A 23 -48.75 -168.98 REMARK 500 3 ASP A 24 38.68 -78.18 REMARK 500 3 SER A 34 -8.71 -58.48 REMARK 500 3 MET A 51 71.50 -103.39 REMARK 500 3 HIS A 52 -70.53 -67.28 REMARK 500 3 THR A 121 -58.82 -132.98 REMARK 500 4 GLU A 23 -60.33 -158.89 REMARK 500 4 ASP A 24 38.84 -78.61 REMARK 500 4 SER A 34 -8.66 -59.31 REMARK 500 4 ASN A 42 13.23 53.82 REMARK 500 4 MET A 51 71.74 -109.75 REMARK 500 4 PHE A 104 -174.74 -65.55 REMARK 500 4 THR A 121 -58.55 -152.84 REMARK 500 5 GLU A 23 -48.24 -158.23 REMARK 500 5 ASP A 24 38.48 -78.18 REMARK 500 5 SER A 34 -8.81 -59.24 REMARK 500 5 ASN A 42 13.00 53.79 REMARK 500 5 MET A 51 50.16 -109.23 REMARK 500 5 LYS A 105 -0.98 -140.89 REMARK 500 5 VAL A 116 -57.14 -129.22 REMARK 500 5 THR A 121 -58.49 -138.69 REMARK 500 6 GLU A 23 -48.59 -158.32 REMARK 500 6 ASP A 24 37.74 -78.61 REMARK 500 6 ASN A 42 13.06 54.08 REMARK 500 6 LYS A 105 -0.78 -141.64 REMARK 500 6 THR A 121 -58.00 -130.17 REMARK 500 7 GLU A 23 -48.71 -158.66 REMARK 500 7 ASP A 24 38.06 -78.77 REMARK 500 7 MET A 51 71.48 -112.11 REMARK 500 7 THR A 121 -58.41 -129.42 REMARK 500 8 GLU A 23 -61.27 -159.63 REMARK 500 8 ASP A 24 38.72 -81.55 REMARK 500 8 ASN A 42 12.88 53.84 REMARK 500 8 MET A 51 71.23 -108.78 REMARK 500 8 PRO A 79 89.73 -69.49 REMARK 500 8 LYS A 105 -0.56 -141.44 REMARK 500 8 VAL A 116 -56.88 -128.57 REMARK 500 8 THR A 121 -77.61 -136.86 REMARK 500 9 GLU A 23 -59.33 -159.20 REMARK 500 9 ASP A 24 39.21 -78.83 REMARK 500 REMARK 500 THIS ENTRY HAS 112 RAMACHANDRAN OUTLIERS. 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 2 ARG A 108 0.09 SIDE CHAIN REMARK 500 3 ARG A 60 0.22 SIDE CHAIN REMARK 500 3 ARG A 103 0.08 SIDE CHAIN REMARK 500 4 ARG A 60 0.13 SIDE CHAIN REMARK 500 4 ARG A 63 0.09 SIDE CHAIN REMARK 500 4 ARG A 108 0.11 SIDE CHAIN REMARK 500 5 ARG A 60 0.16 SIDE CHAIN REMARK 500 5 ARG A 63 0.09 SIDE CHAIN REMARK 500 6 ARG A 60 0.14 SIDE CHAIN REMARK 500 6 ARG A 63 0.10 SIDE CHAIN REMARK 500 6 ARG A 92 0.17 SIDE CHAIN REMARK 500 7 ARG A 76 0.08 SIDE CHAIN REMARK 500 8 ARG A 60 0.10 SIDE CHAIN REMARK 500 8 ARG A 76 0.09 SIDE CHAIN REMARK 500 8 ARG A 108 0.09 SIDE CHAIN REMARK 500 9 ARG A 60 0.12 SIDE CHAIN REMARK 500 9 ARG A 108 0.14 SIDE CHAIN REMARK 500 10 ARG A 60 0.17 SIDE CHAIN REMARK 500 11 ARG A 60 0.22 SIDE CHAIN REMARK 500 11 ARG A 108 0.09 SIDE CHAIN REMARK 500 14 ARG A 60 0.13 SIDE CHAIN REMARK 500 14 ARG A 92 0.24 SIDE CHAIN REMARK 500 15 ARG A 43 0.09 SIDE CHAIN REMARK 500 15 ARG A 60 0.13 SIDE CHAIN REMARK 500 15 ARG A 71 0.14 SIDE CHAIN REMARK 500 15 ARG A 108 0.09 SIDE CHAIN REMARK 500 16 ARG A 60 0.14 SIDE CHAIN REMARK 500 16 ARG A 63 0.09 SIDE CHAIN REMARK 500 17 HIS A 52 0.13 SIDE CHAIN REMARK 500 17 ARG A 60 0.14 SIDE CHAIN REMARK 500 17 ARG A 86 0.09 SIDE CHAIN REMARK 500 17 ARG A 92 0.08 SIDE CHAIN REMARK 500 17 ARG A 108 0.11 SIDE CHAIN REMARK 500 18 ARG A 71 0.24 SIDE CHAIN REMARK 500 19 ARG A 60 0.12 SIDE CHAIN REMARK 500 19 ARG A 92 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FMN REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: FMN BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 123 DBREF 1AXJ A 1 122 UNP Q46604 FMNB_DESVM 1 122 SEQRES 1 A 122 MET LEU PRO GLY THR PHE PHE GLU VAL LEU LYS ASN GLU SEQRES 2 A 122 GLY VAL VAL ALA ILE ALA THR GLN GLY GLU ASP GLY PRO SEQRES 3 A 122 HIS LEU VAL ASN THR TRP ASN SER TYR LEU LYS VAL LEU SEQRES 4 A 122 ASP GLY ASN ARG ILE VAL VAL PRO VAL GLY GLY MET HIS SEQRES 5 A 122 LYS THR GLU ALA ASN VAL ALA ARG ASP GLU ARG VAL LEU SEQRES 6 A 122 MET THR LEU GLY SER ARG LYS VAL ALA GLY ARG ASN GLY SEQRES 7 A 122 PRO GLY THR GLY PHE LEU ILE ARG GLY SER ALA ALA PHE SEQRES 8 A 122 ARG THR ASP GLY PRO GLU PHE GLU ALA ILE ALA ARG PHE SEQRES 9 A 122 LYS TRP ALA ARG ALA ALA LEU VAL ILE THR VAL VAL SER SEQRES 10 A 122 ALA GLU GLN THR LEU HET FMN A 123 50 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P HELIX 1 1 GLY A 4 LEU A 10 1 7 HELIX 2 2 ASN A 33 TYR A 35 5 3 HELIX 3 3 HIS A 52 ARG A 60 1 9 HELIX 4 4 GLY A 95 ALA A 102 1 8 SHEET 1 A 6 HIS A 27 TRP A 32 0 SHEET 2 A 6 VAL A 15 THR A 20 -1 N THR A 20 O HIS A 27 SHEET 3 A 6 ARG A 63 SER A 70 -1 N THR A 67 O ALA A 17 SHEET 4 A 6 THR A 81 ARG A 92 -1 N GLY A 87 O VAL A 64 SHEET 5 A 6 ALA A 109 GLN A 120 -1 N GLU A 119 O LEU A 84 SHEET 6 A 6 ARG A 43 VAL A 48 -1 N VAL A 48 O ALA A 109 SHEET 1 B 1 LYS A 37 VAL A 38 0 SITE 1 FMN 8 TRP A 32 THR A 31 ASN A 30 TRP A 106 SITE 2 FMN 8 PRO A 47 VAL A 48 GLY A 50 LYS A 53 SITE 1 AC1 15 HIS A 27 VAL A 29 ASN A 30 THR A 31 SITE 2 AC1 15 TRP A 32 TYR A 35 PRO A 47 VAL A 48 SITE 3 AC1 15 GLY A 49 GLY A 50 MET A 51 HIS A 52 SITE 4 AC1 15 LYS A 53 THR A 54 TRP A 106 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