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- PDB-5auk: Crystal structure of the Ga-substituted Ferredoxin -

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Basic information

Entry
Database: PDB / ID: 5auk
TitleCrystal structure of the Ga-substituted Ferredoxin
ComponentsFerredoxin-1
KeywordsELECTRON TRANSPORT / Analogue / electron transfer protein
Function / homology
Function and homology information


electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / Beta-grasp domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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) ...Ferredoxin [2Fe-2S], plant / Beta-grasp domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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
BENZAMIDINE / [2Ga-2S] cluster / Ferredoxin-1
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKurisu, G. / Muraki, N. / Taya, M. / Hase, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Cabinet office of JapanGS016 Japan
CitationJournal: Biochemistry / Year: 2015
Title: X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin
Authors: Mutoh, R. / Muraki, N. / Shinmura, K. / Kubota-Kawai, H. / Lee, Y.H. / Nowaczyk, M.M. / Rogner, M. / Hase, T. / Ikegami, T. / Kurisu, G.
History
DepositionApr 24, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,35410
Polymers10,2371
Non-polymers1,1179
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area4950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.942, 31.942, 320.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Ferredoxin-1 / Ferredoxin I


Mass: 10237.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: petF, fed / Production host: Escherichia coli (E. coli) / References: UniProt: P27320
#2: Chemical ChemComp-GAK / [2Ga-2S] cluster


Mass: 203.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ga2S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3.4 M ammonium sulfate, 2% (w/v) benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.62→40 Å / Num. obs: 13883 / % possible obs: 96.6 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 64.1
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 10.2 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OFF

1off


Resolution: 1.62→27.56 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.12 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21923 660 5 %RANDOM
Rwork0.1977 ---
obs0.19874 12598 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.62→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 68 36 811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02793
X-RAY DIFFRACTIONr_bond_other_d0.0010.02684
X-RAY DIFFRACTIONr_angle_refined_deg1.9212.0691077
X-RAY DIFFRACTIONr_angle_other_deg0.93831571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.707599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48126.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7715113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.977151
X-RAY DIFFRACTIONr_chiral_restr0.1310.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
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_it1.4021.421387
X-RAY DIFFRACTIONr_mcbond_other1.3981.421386
X-RAY DIFFRACTIONr_mcangle_it1.9232.133483
X-RAY DIFFRACTIONr_mcangle_other1.9212.133484
X-RAY DIFFRACTIONr_scbond_it3.0182.079405
X-RAY DIFFRACTIONr_scbond_other3.0142.083406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.112.994591
X-RAY DIFFRACTIONr_long_range_B_refined6.90814.706920
X-RAY DIFFRACTIONr_long_range_B_other6.90414.73921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.619→1.661 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 52 -
Rwork0.168 852 -
obs--94.36 %
Refinement TLS params.Method: refined / Origin x: 2.689 Å / Origin y: 6.9887 Å / Origin z: -11.3586 Å
111213212223313233
T0.0251 Å2-0.02 Å20.0161 Å2-0.0526 Å2-0.0302 Å2--0.0206 Å2
L2.732 °20.0021 °20.5092 °2-1.2354 °2-0.0301 °2--1.7745 °2
S0.0177 Å °-0.1716 Å °0.0995 Å °-0.0813 Å °0.0107 Å °-0.0324 Å °-0.1396 Å °-0.0206 Å °-0.0285 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 96
2X-RAY DIFFRACTION1A101

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