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- PDB-6gm6: [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141Q -

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Basic information

Entry
Database: PDB / ID: 6gm6
Title[FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141Q
ComponentsFe-hydrogenase
KeywordsHYDROLASE / Hydrogenase / H-cluster / apo-form / oxidoreductase
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: 1.61 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.3May 15, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)49,2874
Polymers48,8771
Non-polymers4103
Water9,602533
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 area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.790, 70.790, 155.030
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-1144-

HOH

21A-1209-

HOH

31A-1217-

HOH

41A-1231-

HOH

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Components

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


Mass: 48876.738 Da / Num. of mol.: 1 / Fragment: apo enzyme / Mutation: E141Q
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.: 533 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG 4000, 0.6 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972958 Å / Relative weight: 1
ReflectionResolution: 1.61→48.1062 Å / Num. obs: 59107 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.822 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.61-1.651.21620.6591100
1.65-1.70.9762.490.7581100
1.7-1.750.7623.080.8331100
1.75-1.80.6043.960.9041100
1.8-1.860.4685.330.9411100
1.86-1.920.3936.260.9581100
1.92-20.3038.010.9711100
2-2.080.2459.490.9821100
2.08-2.170.19411.630.9881100
2.17-2.280.16813.180.99199.9
2.28-2.40.14314.860.9921100
2.4-2.550.12316.390.993199.8
2.55-2.720.11219.390.9951100
2.72-2.940.09622.30.9961100
2.94-3.220.08325.030.9971100
3.22-3.60.0728.910.9971100
3.6-4.160.06530.480.9971100
4.16-5.090.05930.570.997199.3
5.09-7.20.06233.250.9981100
7.2-48.0850.05933.740.998199.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.61→48.085 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.25
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2970 5.03 %random selection
Rwork0.1639 ---
obs0.1657 59100 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 26.4619 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.61→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 10 533 3641
Biso mean--17.68 38.6 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073194
X-RAY DIFFRACTIONf_angle_d1.0344318
X-RAY DIFFRACTIONf_chiral_restr0.042482
X-RAY DIFFRACTIONf_plane_restr0.005560
X-RAY DIFFRACTIONf_dihedral_angle_d13.3571191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.61-1.63640.31281400.268626312771
1.6364-1.66460.2731410.245626142755
1.6646-1.69490.27231410.227926302771
1.6949-1.72750.23581410.211126742815
1.7275-1.76280.26891390.203326442783
1.7628-1.80110.22751390.189626392778
1.8011-1.8430.20781370.182826182755
1.843-1.88910.2151430.181526412784
1.8891-1.94020.20981370.171626542791
1.9402-1.99730.23111390.173326502789
1.9973-2.06170.21241380.167626352773
2.0617-2.13540.19761410.16226752816
2.1354-2.22090.20471400.154926792819
2.2209-2.3220.18971390.151626432782
2.322-2.44440.18511430.159227012844
2.4444-2.59760.20921440.164926602804
2.5976-2.79810.17521410.166226872828
2.7981-3.07960.19471450.16127132858
3.0796-3.52520.18651400.148327142854
3.5252-4.44080.1611440.132927542898
4.4408-48.10620.19951580.164528743032

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