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- PDB-4id8: The crystal structure of a [3Fe-4S] ferredoxin associated with CY... -

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Basic information

Entry
Database: PDB / ID: 4id8
TitleThe crystal structure of a [3Fe-4S] ferredoxin associated with CYP194A4 from R. palustris HaA2
ComponentsPutative ferredoxin
KeywordsELECTRON TRANSPORT / 4Fe-4S single cluster domain
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
4Fe-4S single cluster domain / : / Alpha-Beta Plaits - #20 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / Putative ferredoxin
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhou, 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. / Bell, S.G. / Wong, L.L. / Zhou, W.
History
DepositionDec 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Sep 20, 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
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.354, 26.699, 91.094
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


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


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.87 Å3/Da / Density % sol: 34.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.3 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5, 2.4 M 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: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 3425 / Num. obs: 3298 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.086 / Net I/σ(I): 16.4
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 7.9 / Num. unique all: 323 / Rsym value: 0.133 / % possible all: 76.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8Q

2z8q


Resolution: 2.15→45.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.385 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.307 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27509 141 4.3 %RANDOM
Rwork0.19255 ---
obs0.19591 3105 95.67 %-
all-3246 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.635 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å2-0 Å20 Å2
2--5.79 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms497 0 7 19 523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021518
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0772.006723
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.158564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92826.92326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3511583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.293151
X-RAY DIFFRACTIONr_chiral_restr0.140.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.981.5323
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7892515
X-RAY DIFFRACTIONr_scbond_it2.8813195
X-RAY DIFFRACTIONr_scangle_it4.7544.5181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 9 -
Rwork0.231 171 -
obs--74.38 %

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