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- PDB-6gm5: [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141A -

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Basic information

Entry
Database: PDB / ID: 6gm5
Title[FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141A
ComponentsFe-hydrogenase
KeywordsHYDROLASE / Hydrogenase / H-cluster / apo-form
Function / homology
Function and homology information


1.18.99.1 / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain ...Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Fe-hydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDuan, J. / Engelbrecht, V. / Esselborn, J. / Hofmann, E. / Winkler, M. / Happe, T.
CitationJournal: Nat Commun / Year: 2018
Title: Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases.
Authors: Duan, J. / Senger, M. / Esselborn, J. / Engelbrecht, V. / Wittkamp, F. / Apfel, U.P. / Hofmann, E. / Stripp, S.T. / Happe, T. / Winkler, M.
History
DepositionMay 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2304
Polymers48,8201
Non-polymers4103
Water10,395577
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-43 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.620, 70.620, 154.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1166-

HOH

21A-1249-

HOH

31A-1262-

HOH

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Components

#1: Protein Fe-hydrogenase / Iron hydrogenase / Iron-hydrogenase HydA1


Mass: 48819.684 Da / Num. of mol.: 1 / Fragment: apo enzyme / Mutation: E141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant)
Gene: hyd1, HYD1, hydA, hydA1, CHLRE_03g199800v5, CHLREDRAFT_183963
Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): DiscR / References: UniProt: Q9FYU1, 1.18.99.1
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 11% PEG 4000, 0.5 M NaCl,0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.972958 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972958 Å / Relative weight: 1
ReflectionResolution: 1.45→48 Å / Num. obs: 79955 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 18.38 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.11
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.45-1.491.0792.240.723197.2
1.49-1.530.9093.10.868199.8
1.53-1.570.764.590.9281100
1.57-1.620.6246.130.9611100
1.62-1.670.4947.680.9771100
1.67-1.730.389.750.9861100
1.73-1.80.30411.840.9911100
1.8-1.870.23615.450.9951100
1.87-1.960.18818.920.9961100
1.96-2.050.14822.930.9971100
2.05-2.160.11527.340.9981100
2.16-2.290.097330.9981100
2.29-2.450.08337.630.9991100
2.45-2.650.07540.170.9991100
2.65-2.90.06445.490.9991100
2.9-3.240.05652.360.9991100
3.24-3.740.04859.090.9991100
3.74-4.590.04461.020.9991100
4.59-6.480.04561.910.999199.9
6.48-47.9990.04360.721199.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX4

3lx4


Resolution: 1.45→47.999 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.98
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 4004 5.01 %random selection
Rwork0.1653 ---
obs0.1668 79944 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.89 Å2 / Biso mean: 26.2838 Å2 / Biso min: 9.81 Å2
Refinement stepCycle: final / Resolution: 1.45→47.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 10 577 3681
Biso mean--16.57 38.29 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093191
X-RAY DIFFRACTIONf_angle_d1.2244313
X-RAY DIFFRACTIONf_chiral_restr0.052482
X-RAY DIFFRACTIONf_plane_restr0.006559
X-RAY DIFFRACTIONf_dihedral_angle_d12.8361188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4501-1.46710.28791270.27572505263296
1.4671-1.4850.31751360.25652527266398
1.485-1.50380.2541350.24722588272399
1.5038-1.52360.281330.231725642697100
1.5236-1.54450.24951400.21326212761100
1.5445-1.56650.2841340.20626162750100
1.5665-1.58990.21231350.201125482683100
1.5899-1.61480.22371320.189425992731100
1.6148-1.64120.22451420.18126202762100
1.6412-1.66950.21791370.181825632700100
1.6695-1.69990.18921430.172926262769100
1.6999-1.73260.23351380.170525962734100
1.7326-1.7680.20581360.172626132749100
1.768-1.80640.19991370.170926012738100
1.8064-1.84840.20371350.164225982733100
1.8484-1.89470.18911380.165525992737100
1.8947-1.94590.19411380.165626062744100
1.9459-2.00320.20761390.170126302769100
2.0032-2.06780.19151350.167526032738100
2.0678-2.14170.19281380.162326392777100
2.1417-2.22750.19041370.156226132750100
2.2275-2.32880.17661380.150726192757100
2.3288-2.45160.19391410.162526532794100
2.4516-2.60520.21721410.163826352776100
2.6052-2.80630.17211380.166226392777100
2.8063-3.08870.20071440.162926772821100
3.0887-3.53550.1841410.150326842825100
3.5355-4.45390.17511410.134127192860100
4.4539-48.02570.18981550.173528392994100

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