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- PDB-1ofv: FLAVODOXIN FROM ANACYSTIS NIDULANS: REFINEMENT OF TWO FORMS OF TH... -

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Basic information

Entry
Database: PDB / ID: 1ofv
TitleFLAVODOXIN FROM ANACYSTIS NIDULANS: REFINEMENT OF TWO FORMS OF THE OXIDIZED PROTEIN
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


FMN binding / electron transfer activity
Similarity search - Function
Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold ...Flavodoxin, long chain / : / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavodoxin
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSmith, W.W. / Pattridge, K.A. / Luschinsky, C.L. / Ludwig, M.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Refined structures of oxidized flavodoxin from Anacystis nidulans.
Authors: Drennan, C.L. / Pattridge, K.A. / Weber, C.H. / Metzger, A.L. / Hoover, D.M. / Ludwig, M.L.
#1: Journal: Flavins and Flavoproteins / Year: 1991
Title: Structural Analysis of Fully Reduced A. Nidulans Flavodoxin
Authors: Luschinsky, C.L. / Dunham, W.R. / Osborne, C. / Pattridge, K.A. / Ludwig, M.L.
#2: Journal: Flavins and Flavoproteins / Year: 1987
Title: Sequence and Structure of Anacystis Nidulans Flavodoxin: Comparisons with Flavodoxins from Other Species
Authors: Laudenbach, D.E. / Straus, N.A. / Pattridge, K.A. / Ludwig, M.L.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Oxidized Flavodoxin from Anacystis Nidulans
Authors: Smith, W.W. / Pattridge, K.A. / Ludwig, M.L. / Petsko, G.A. / Tsernoglou, D. / Tanaka, M. / Yasunobu, K.T.
History
DepositionJun 22, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON DSSP OUTPUT (KABSCH AND SANDER, 1983) WITH ...HELIX ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON DSSP OUTPUT (KABSCH AND SANDER, 1983) WITH THE FOLLOWING EXCEPTIONS: HELICES START WITH THE FIRST RESIDUE HAVING ONE HELICAL HYDROGEN BOND; SUCCESSIVE 3-10 TURNS ARE GIVEN PRIORITY OVER SHORT 3-10 HELICES. TWO SHORT ANTIPARALLEL HAIRPINS OCCUR IN THIS FLAVODOXIN AND TWO HELICES END WITH COMBINATIONS OF 4- AND 2-RESIDUE TURNS, SO-CALLED PAPERCLIPS.
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, AND 4 OF B1 AND B2 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1132
Polymers18,6561
Non-polymers4561
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.080, 69.240, 45.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FLAVODOXIN


Mass: 18656.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / References: UniProt: P10340
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FOLLOWING ARE NOT STANDARD TURNS: TURN 1 GLN 22 GLY 27 4 RESIDUE TURN TURN 5 TRP 57 GLU 61 3 ...THE FOLLOWING ARE NOT STANDARD TURNS: TURN 1 GLN 22 GLY 27 4 RESIDUE TURN TURN 5 TRP 57 GLU 61 3 RES TURN IN 56-62 HAIRPIN TURN 7 ASP 90 TYR 94 3 RESIDUE TURN TURN 13 ASP 144 GLN 148 3 RESIDUE TURN TURN 16 LYS 164 LEU 169 4 RESIDUE TURN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.7 Å / σ(F): 0 /
RfactorNum. reflection
obs0.19 20059
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 31 89 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.012
X-RAY DIFFRACTIONp_angle_d0.0360.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1241
X-RAY DIFFRACTIONp_mcangle_it1.7631.5
X-RAY DIFFRACTIONp_scbond_it1.7511
X-RAY DIFFRACTIONp_scangle_it2.9291.5
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.2060.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.5
X-RAY DIFFRACTIONp_multtor_nbd0.1760.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2230.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.7631.5
X-RAY DIFFRACTIONp_staggered_tor1.7511
X-RAY DIFFRACTIONp_orthonormal_tor2.9291.5
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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