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- PDB-1rcf: STRUCTURE OF THE TRIGONAL FORM OF RECOMBINANT OXIDIZED FLAVODOXIN... -

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Basic information

Entry
Database: PDB / ID: 1rcf
TitleSTRUCTURE OF THE TRIGONAL FORM OF RECOMBINANT OXIDIZED FLAVODOXIN FROM ANABAENA 7120 AT 1.40 ANGSTROMS RESOLUTION
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSFER(FLAVOPROTEIN)
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 speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsBurkhart, B. / Ramakrishnan, B. / Yan, H. / Reedstrom, R. / Markley, J. / Straus, N. / Sundaralingam, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of the trigonal form of recombinant oxidized flavodoxin from Anabaena 7120 at 1.40 A resolution.
Authors: Burkhart, B.M. / Ramakrishnan, B. / Yan, H. / Reedstrom, R.J. / Markley, J.L. / Straus, N.A. / Sundaralingam, M.
#1: Journal: Protein Sci. / Year: 1992
Title: Structure of the Oxidized Long-Chain Flavodoxin from Anabaena 7120 at 2 Angstroms Resolution
Authors: Rao, S. / Shaffie, F. / Yu, C. / Satyshur, K. / Stockman, B. / Markley, J. / Sundaralingam, M.
History
DepositionOct 31, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLAVODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4003
Polymers18,8481
Non-polymers5522
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.360, 55.360, 102.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-437-

HOH

31A-438-

HOH

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Components

#1: Protein FLAVODOXIN


Mass: 18847.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Plasmid: PGEM-AVF AND PGPI-2 / References: UniProt: P0A3D9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
180 mg/mlprotein1drop
2200 mMTris-HCl1drop
380 %satammonium sulfate1drop
43.3 Mammonium sulfate1reservoir

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Data collection

ReflectionNum. obs: 36069 / % possible obs: 99.1 %
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 9999 Å / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.51 Å / % possible obs: 94.3 % / Num. unique obs: 6774

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Processing

Software
NameClassification
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
SHELXL-97phasing
X-PLORphasing
RefinementHighest resolution: 1.4 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.139 --
obs0.139 32963 90 %
Displacement parametersBiso mean: 17.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: LAST / Highest resolution: 1.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 36 299 1667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR/SHELXL93 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_d0.030.015
X-RAY DIFFRACTIONx_plane_restr0.2740.191
X-RAY DIFFRACTIONx_chiral_restr0.20.092

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