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- PDB-2fcr: CRYSTAL STRUCTURE OF OXIDIZED FLAVODOXIN FROM A RED ALGA CHONDRUS... -

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Basic information

Entry
Database: PDB / ID: 2fcr
TitleCRYSTAL STRUCTURE OF OXIDIZED FLAVODOXIN FROM A RED ALGA CHONDRUS CRISPUS REFINED AT 1.8 ANGSTROMS RESOLUTION: DESCRIPTION OF THE FLAVIN MONONUCLEOTIDE BINDING SITE
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 speciesChondrus crispus (carragheen)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFukuyama, K.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure of oxidized flavodoxin from a red alga Chondrus crispus refined at 1.8 A resolution. Description of the flavin mononucleotide binding site
Authors: Fukuyama, K. / Matsubara, H. / Rogers, L.J.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Tertiary Structure of Oxidized Flavodoxin from an Eukaryotic Red Alga Chondrus Crispus at 2.35-Angstroms Resolution. Localization of Charged Residues and Implication for Interaction with Electron Transfer Partners
Authors: Fukuyama, K. / Wakabayashi, S. / Matsubara, H. / Rogers, L.J.
#2: Journal: J.Biochem.(Tokyo) / Year: 1989
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Oxidized Flavodoxin from Chondrus Crispus, a Red Alga
Authors: Fukuyama, K. / Matsubara, H. / Katsube, Y. / Rogers, L.J.
#3: Journal: Biochem.J. / Year: 1989
Title: The Amino Acid Sequence of a Flavodoxin from the Eukaryotic Red Alga Chondrus Crispus
Authors: Wakabayashi, S. / Kimura, T. / Fukuyama, K. / Matsubara, H. / Rogers, L.J.
History
DepositionFeb 3, 1992Processing site: BNL
Revision 1.0Mar 4, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)19,3422
Polymers18,8861
Non-polymers4561
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.570, 48.830, 56.830
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: 18885.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chondrus crispus (carragheen) / References: UniProt: P14070
#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.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / Rfactor obs: 0.188 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 31 110 1471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0280.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.651
X-RAY DIFFRACTIONp_mcangle_it1.011.5
X-RAY DIFFRACTIONp_scbond_it1.581.5
X-RAY DIFFRACTIONp_scangle_it2.42
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1460.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.5
X-RAY DIFFRACTIONp_multtor_nbd0.180.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.150.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.23
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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