2FZ5 - Header Asymmetric Unit

HEADER ELECTRON TRANSPORT 09-FEB-06 2FZ5

TITLE SOLUTION STRUCTURE OF TWO-ELECTRON REDUCED MEGASPHAERA TITLE 2 ELSDENII FLAVODOXIN

COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MEGASPHAERA ELSDENII; SOURCE 3 ORGANISM_TAXID: 907

KEYWDS ALPHA/BETA DOUBLY-WOUND TOPOLOGY, NON-COVALENTLY BOUND FMN, KEYWDS 2 ELECTRON TRANSPORT

EXPDTA SOLUTION NMR

AUTHOR C.P.M.VAN MIERLO,P.LIJNZAAD,J.VERVOORT,F.MUELLER, AUTHOR 2 H.J.BERENDSEN,J.DE VLIEG

REVDAT 3 24-FEB-09 2FZ5 1 VERSN REVDAT 2 11-APR-06 2FZ5 1 FORMUL REVDAT 1 14-MAR-06 2FZ5 0

JRNL AUTH C.P.M.VAN MIERLO,P.LIJNZAAD,J.VERVOORT,F.MUELLER, JRNL AUTH 2 H.J.BERENDSEN,J.DE VLIEG JRNL TITL TERTIARY STRUCTURE OF TWO-ELECTRON REDUCED JRNL TITL 2 MEGASPHAERA ELSDENII FLAVODOXIN AND SOME JRNL TITL 3 IMPLICATIONS, AS DETERMINED BY TWO-DIMENSIONAL 1H JRNL TITL 4 NMR AND RESTRAINED MOLECULAR DYNAMICS JRNL REF EUR.J.BIOCHEM. V. 194 185 1990 JRNL REFN ISSN 0014-2956 JRNL PMID 2253614 JRNL DOI 10.1111/J.1432-1033.1990.TB19444.X

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.P.M.VAN MIERLO,F.MUELLER,J.VERVOORT REMARK 1 TITL SECONDARY AND TERTIARY STRUCTURE CHARACTERISTICS REMARK 1 TITL 2 OF MEGASPHAERA ELSDENII FLAVODOXIN IN THE REDUCED REMARK 1 TITL 3 STATE AS DETERMINED BY TWO-DIMENSIONAL 1H NMR REMARK 1 REF EUR.J.BIOCHEM. V. 189 589 1990 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 2161759 REMARK 1 DOI 10.1111/J.1432-1033.1990.TB15527.X REMARK 1 REFERENCE 2 REMARK 1 AUTH C.P.M.VAN MIERLO,J.VERVOORT,F.MUELLER,A.BACHER REMARK 1 TITL A TWO-DIMENSIONAL 1H NMR STUDY ON MEGASPHAERA REMARK 1 TITL 2 ELSDENII FLAVODOXIN IN THE REDUCED STATE: REMARK 1 TITL 3 SEQUENTIAL ASSIGNMENTS REMARK 1 REF EUR.J.BIOCHEM. V. 187 521 1990 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 2303055 REMARK 1 DOI 10.1111/J.1432-1033.1990.TB15334.X REMARK 1 REFERENCE 3 REMARK 1 AUTH C.P.M.VAN MIERLO,B.P.VAN DER SANDEN,P.VAN WOENSEL, REMARK 1 AUTH 2 F.MUELLER,J.VERVOORT REMARK 1 TITL A TWO-DIMENSIONAL 1H NMR STUDY ON MEGASPHAERA REMARK 1 TITL 2 ELSDENII FLAVODOXIN IN THE OXIDIZED STATE AND SOME REMARK 1 TITL 3 COMPARISONS WITH THE TWO-ELECTRON REDUCED STATE REMARK 1 REF EUR.J.BIOCHEM. V. 194 199 1990 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 2253616 REMARK 1 DOI 10.1111/J.1432-1033.1990.TB19445.X

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMOS REMARK 3 AUTHORS : VAN GUNSTEREN AND BERENDSEN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE XRAY STRUCTURE OF THE REMARK 3 SEMIQUINONE STATE OF CLOSTRIDIUM MP FLAVODOXIN WAS USED AS A REMARK 3 STARTING STRUCTURE FOR RESTRAINED MOLECULAR DYNAMICS (RMD) REMARK 3 CALCULATIONS IN VACUO (VAN MIERLO ET AL. EUR. J. BIOCHEM. 194, REMARK 3 185 - 198 (1990)). 509 DISTANCE RESTRAINTS, 293 MEDIUM, 216 REMARK 3 LONG-RANGE WERE USED IN REFINEMENT. ONE REPULSIVE RESTRAINT, REMARK 3 BETWEEN N5H OF FMN AND NH OF E60 WAS INCLUDED. RMD RUN WAS OF REMARK 3 120 PS. DURING THE FIRST 50 PS THE FORCE CONSTANT WAS REMARK 3 GRADUALLY INCREASED TO A HIGH VALUE OF 4000 KJMOL-1NM-2. FROM REMARK 3 50 PS ON, THE FORCE CONSTANT WAS KEPT CONSTANT. THE TIME SPAN REMARK 3 OF 60-120 PS, AT A TIME RESOLUTION OF 0.02 PS, WAS USED FOR REMARK 3 CALCULATING THE AVERAGE STRUCTURE. THE TIME-AVERAGED (NOT REMARK 3 ENERGY MINIMISED) STRUCTURE HAS A POTENTIAL ENERGY -2278 +/- REMARK 3 122 KJMOL-1, TIME-AVERAGED SUM OF ALL VIOLATIONS IS 2.27 NM, REMARK 3 LARGEST OCCURING VIOLATION IS 66 PM

REMARK 4 REMARK 4 2FZ5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-06. REMARK 100 THE RCSB ID CODE IS RCSB036485.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 306; 310; 314; 316 REMARK 210 PH : 8.3; 8.3; 8.3; 8.3; 8.3 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL; NULL; NULL REMARK 210 PRESSURE : NULL; NULL; NULL; NULL; NULL REMARK 210 SAMPLE CONTENTS : 6-10 MM PROTEIN, POTASSIUM REMARK 210 PHOSPHATE/POTASSIUM REMARK 210 PYROPHOSPHATE 75-200 MM, PH REMARK 210 8.3, 90% H2O, 10% D2O; 6-10 MM REMARK 210 PROTEIN, POTASSIUM PHOSPHATE/ REMARK 210 POTASSIUM PYROPHOSPHATE 75-200 REMARK 210 MM, PH 8.3, 99.9% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY, DOUBLE QUANTUM FILTERED REMARK 210 COSY, NOESY (MIXING 200MS), REMARK 210 NOESY (MIXING 50, 100, 150 MS) REMARK 210 , DOUBLE QUANTUM SPECTRA, REMARK 210 HOMONUCLEAR HARTMANN HAHN REMARK 210 TRANSFER SPECTRA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : WM, AM REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DISNMR, GROMOS REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 3000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NOESY SPECTRA HAD MIXING TIMES 50, 100, 150 AND 200 MS. REMARK 210 DOUBLE QUANTUM SPECTRA HAD A DELAY OF 32 MS. HOMONUCLEAR REMARK 210 HARTMANN HAHN TRANSFER SPECTRA (USING MLEV-17 COMPOSITE PULSE REMARK 210 CYCLING) HAD MIXING TIMES 10-160 MS

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 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 ASN A 118 OD1 - CG - ND2 ANGL. DEV. = -25.0 DEGREES REMARK 500 ASN A 118 CB - CG - OD1 ANGL. DEV. = 14.1 DEGREES REMARK 500 ASN A 118 CB - CG - ND2 ANGL. DEV. = -15.9 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 VAL A 66 -59.74 -122.38 REMARK 500 LEU A 78 59.95 -107.44 REMARK 500 LYS A 81 152.19 -49.43 REMARK 500 ILE A 112 53.61 -90.64 REMARK 500 GLU A 119 -73.62 62.31 REMARK 500 PRO A 121 -177.13 -63.04 REMARK 500 ASP A 122 -37.11 72.66 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 ARG A 35 0.11 SIDE_CHAIN REMARK 500 PHE A 70 0.08 SIDE_CHAIN REMARK 500 PHE A 71 0.08 SIDE_CHAIN REMARK 500 ASN A 118 0.16 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, 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 TRP A 96 -10.76 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 FNR A 138

DBREF 2FZ5 A 1 137 UNP P00321 FLAV_MEGEL 1 137

SEQRES 1 A 137 MET VAL GLU ILE VAL TYR TRP SER GLY THR GLY ASN THR SEQRES 2 A 137 GLU ALA MET ALA ASN GLU ILE GLU ALA ALA VAL LYS ALA SEQRES 3 A 137 ALA GLY ALA ASP VAL GLU SER VAL ARG PHE GLU ASP THR SEQRES 4 A 137 ASN VAL ASP ASP VAL ALA SER LYS ASP VAL ILE LEU LEU SEQRES 5 A 137 GLY CYS PRO ALA MET GLY SER GLU GLU LEU GLU ASP SER SEQRES 6 A 137 VAL VAL GLU PRO PHE PHE THR ASP LEU ALA PRO LYS LEU SEQRES 7 A 137 LYS GLY LYS LYS VAL GLY LEU PHE GLY SER TYR GLY TRP SEQRES 8 A 137 GLY SER GLY GLU TRP MET ASP ALA TRP LYS GLN ARG THR SEQRES 9 A 137 GLU ASP THR GLY ALA THR VAL ILE GLY THR ALA ILE VAL SEQRES 10 A 137 ASN GLU MET PRO ASP ASN ALA PRO GLU CYS LYS GLU LEU SEQRES 11 A 137 GLY GLU ALA ALA ALA LYS ALA

HET FNR A 138 37

HETNAM FNR 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H- HETNAM 2 FNR BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D- HETNAM 3 FNR RIBITOL

HETSYN FNR TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE

FORMUL 2 FNR C17 H23 N4 O9 P

HELIX 1 1 GLY A 11 ALA A 27 1 17 HELIX 2 2 ASN A 40 SER A 46 1 7 HELIX 3 3 GLU A 63 ALA A 75 1 13 HELIX 4 4 PRO A 76 LEU A 78 5 3 HELIX 5 5 GLY A 94 THR A 107 1 14 HELIX 6 6 PRO A 125 LYS A 136 1 12

SHEET 1 A 5 VAL A 31 ARG A 35 0 SHEET 2 A 5 VAL A 2 TYR A 6 1 N VAL A 2 O GLU A 32 SHEET 3 A 5 VAL A 49 GLY A 53 1 O LEU A 51 N VAL A 5 SHEET 4 A 5 LYS A 82 TYR A 89 1 O LYS A 82 N ILE A 50 SHEET 5 A 5 THR A 110 ASN A 118 1 O VAL A 117 N TYR A 89

SITE 1 AC1 15 TRP A 7 GLY A 9 THR A 10 ASN A 12 SITE 2 AC1 15 PRO A 55 ALA A 56 MET A 57 GLY A 58 SITE 3 AC1 15 GLU A 60 SER A 88 TYR A 89 GLY A 90 SITE 4 AC1 15 TRP A 91 GLY A 92 GLU A 119

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