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- PDB-4ltu: Crystal Structure of Ferredoxin from Rhodopseudomonas palustris HaA2 -

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Basic information

Entry
Database: PDB / ID: 4ltu
TitleCrystal Structure of Ferredoxin from Rhodopseudomonas palustris HaA2
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / 2Fe-2S single cluster domain
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZhou, W.H. / Zhang, T. / Yang, H. / Bell, S.G. / Wong, L.-L.
CitationJournal: To be Published
Title: Crystal Structure of Ferredoxin from Rhodopseudomonas palustris HaA2
Authors: Zhou, W.H. / Zhang, T. / Yang, H. / Bell, S.G. / Wong, L.-L.
History
DepositionJul 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _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: Ferredoxin
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2274
Polymers22,8762
Non-polymers3522
Water82946
1
A: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6142
Polymers11,4381
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6142
Polymers11,4381
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.983, 73.145, 78.845
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 Ferredoxin


Mass: 11437.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3614 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2IU01
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01M Cobalt chloride hexahydrate, 0.1M MES pH 6.0, 1.8M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 17, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→53.62 Å / Num. all: 8395 / Num. obs: 8261 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 22.091 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.12 / Net I/σ(I): 7.75
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.42 / Num. unique all: 832 / Rsym value: 0.381 / % possible all: 95

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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: 1R7S

1r7s


Resolution: 2.31→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.841 / SU B: 9.85 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.633 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29775 368 4.5 %RANDOM
Rwork0.22837 ---
obs0.23161 7754 96.97 %-
all-7996 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.091 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2--0.49 Å2-0 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 8 46 1636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_angle_refined_deg1.598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.046
X-RAY DIFFRACTIONr_chiral_restr0.11
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_mcbond_it0.638
X-RAY DIFFRACTIONr_mcangle_it1.148
X-RAY DIFFRACTIONr_scbond_it1.982
X-RAY DIFFRACTIONr_scangle_it3.069
LS refinement shellResolution: 2.308→2.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 25 -
Rwork0.248 537 -
obs--91.68 %

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