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- PDB-4ov1: The crystal structure of a novel electron transfer ferredoxin fro... -

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Basic information

Entry
Database: PDB / ID: 4ov1
TitleThe crystal structure of a novel electron transfer ferredoxin from R. palustris HaA2
ComponentsPutative ferredoxin
KeywordsELECTRON TRANSPORT / 3Fe-4S single cluster domain / putative ferredoxin
Function / homology4Fe-4S single cluster domain / Alpha-Beta Plaits - #20 / 3 iron, 4 sulfur cluster binding / Alpha-Beta Plaits / 2-Layer Sandwich / metal ion binding / Alpha Beta / FE3-S4 CLUSTER / Putative ferredoxin
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsZhouw, W.H. / Zhang, T. / Zhang, A.L. / Bell, S.G. / Wong, L.-L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of a novel electron-transfer ferredoxin from Rhodopseudomonas palustris HaA2 which contains a histidine residue in its iron-sulfur cluster-binding motif.
Authors: Zhang, T. / Zhang, A.L. / Bell, S.G. / Wong, L.-L. / Zhou, W.H.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _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: Putative ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8882
Polymers7,5921
Non-polymers2961
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.362, 26.810, 91.192
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 Putative ferredoxin /


Mass: 7592.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3630 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2ITY5
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3M potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5, 2.4M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 25, 2012 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 2730 / Num. obs: 2832 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.068 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 12.3 / Num. unique all: 147 / Rsym value: 0.126 / % possible all: 80.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8Q

2z8q


Resolution: 2.306→23.111 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 266 9.96 %RANDOM
Rwork0.2226 ---
obs0.2247 2671 94.99 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.37 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.48 Å2
Baniso -1Baniso -2Baniso -3
1--11.3358 Å20 Å2-0 Å2
2--27.3829 Å20 Å2
3----16.0471 Å2
Refinement stepCycle: LAST / Resolution: 2.306→23.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 0 7 13 523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014521
X-RAY DIFFRACTIONf_angle_d1.503704
X-RAY DIFFRACTIONf_dihedral_angle_d12.461191
X-RAY DIFFRACTIONf_chiral_restr0.06377
X-RAY DIFFRACTIONf_plane_restr0.00694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3064-2.90490.34851220.2571111891
2.9049-23.11210.20611440.208128799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.18950.30881.47840.4947-0.10482.91210.0442-0.2777-0.07960.0171-0.02160.0063-0.0397-0.1765-0.04620.17190.00020.0310.25380.01260.2075-0.58237.4107-7.4526
21.3629-2.23070.4194.8116-1.82041.35560.14490.20490.006-0.3304-0.1427-0.0930.0095-0.0415-0.0270.2022-0.02280.00830.2308-0.02080.17310.04486.7685-17.3154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:44)
2X-RAY DIFFRACTION2(chain A and resid 45:69)

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