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- PDB-6gm7: [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E144A -

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Basic information

Entry
Database: PDB / ID: 6gm7
Title[FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E144A
ComponentsFe-hydrogenase
KeywordsOXIDOREDUCTASE / 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 / Resolution: 2.14 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 1.3May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2073
Polymers48,8201
Non-polymers3872
Water6,882382
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-34 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.910, 70.910, 154.800
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-960-

HOH

21A-1044-

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: E144A
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 BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 4000, 0.4 M NaCl,0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 26, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.14→48.1195 Å / Num. obs: 25469 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.165 / Rsym value: 0.179 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.14-2.20.8052.030.476199.8
2.2-2.260.7672.360.534199.8
2.26-2.320.6192.880.691199.8
2.32-2.390.5683.150.733199.8
2.39-2.470.4923.640.788199.9
2.47-2.560.4564.040.824199
2.56-2.650.3954.530.867199.3
2.65-2.760.3485.410.909199.8
2.76-2.890.2936.470.925199.9
2.89-3.030.267.480.957199.9
3.03-3.190.2049.380.974199.7
3.19-3.380.15911.970.983199.5
3.38-3.620.11515.60.992198.7
3.62-3.910.08918.820.995198.2
3.91-4.280.06722.850.997199.2
4.28-4.790.05727.230.998198.9
4.79-5.530.06126.020.997198.6
5.53-6.770.06923.050.997198.2
6.77-9.570.04729.290.999197.2
9.57-48.1070.03438.20.999196.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.14→48.107 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1279 5.02 %random selection
Rwork0.1897 ---
obs0.1916 25466 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.68 Å2 / Biso mean: 30.1692 Å2 / Biso min: 11.25 Å2
Refinement stepCycle: final / Resolution: 2.14→48.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 9 382 3490
Biso mean--19.29 36.85 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033196
X-RAY DIFFRACTIONf_angle_d0.7124330
X-RAY DIFFRACTIONf_chiral_restr0.027484
X-RAY DIFFRACTIONf_plane_restr0.004562
X-RAY DIFFRACTIONf_dihedral_angle_d13.7221193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1401-2.22580.26111390.230126552794100
2.2258-2.32710.27781410.22226372778100
2.3271-2.44980.2861410.223326802821100
2.4498-2.60330.30011400.21082637277799
2.6033-2.80420.23271410.200526662807100
2.8042-3.08640.23831480.189127052853100
3.0864-3.53290.19421380.16482679281799
3.5329-4.45060.18321350.14882709284499
4.4506-48.11950.21231560.20342819297598

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