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- PDB-1czu: REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS -

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Basic information

Entry
Database: PDB / ID: 1czu
TitleREFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS
ComponentsFLAVODOXIN
KeywordsELECTRON TRANSPORT / FLAVODOXIN / FMN BINDING / REDOX POTENTIAL / CRYSTAL PACKING
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: 2 Å
AuthorsDrennan, C.L. / Pattridge, K.A. / Weber, C.H. / Metzger, A.L. / Hoover, D.M. / Ludwig, M.L.
CitationJournal: 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.
History
DepositionSep 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 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)19,1132
Polymers18,6561
Non-polymers4561
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.050, 65.850, 51.360
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
Details: WILDTYPE CRYSTAL FORM II, OXIDIZED / Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Plasmid: PKK233-2-ANFLD / Production host: Escherichia coli (E. coli) / Strain (production host): W1485 / 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.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, POTASSIUM CHLORIDE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.5-10.2 mg/mlprotein1drop
20.96-1.4 Mammonium sulfate1drop
30.06-0.075 mMpotassium phosphate1drop
42.4-2.8 Mammonium sulfate1reservoir
50.15 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 15, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 13513 / Num. obs: 13513 / % possible obs: 90 % / Redundancy: 3.3 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.09 Å / Num. unique all: 1333 / % possible all: 97.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 74 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1285 9.8 %RANDOM
Rwork0.147 ---
obs0.147 13134 92.8 %-
all-13134 --
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 31 116 1465
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.551.5
X-RAY DIFFRACTIONx_mcangle_it2.212
X-RAY DIFFRACTIONx_scbond_it3.422
X-RAY DIFFRACTIONx_scangle_it5.22.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.201 196 10.1 %
Rwork0.175 1738 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.FMNTOPH.FMN
X-RAY DIFFRACTION3PARAM.WATTOPH.WAT
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.201 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.175

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