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- PDB-6gl6: apo [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii, vari... -

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Basic information

Entry
Database: PDB / ID: 6gl6
Titleapo [FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii, variant C377H
ComponentsFe-hydrogenase
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenase / iron sulfur cluster binding
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 ...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 / SULFITE ION / Fe-hydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKertess, L. / Happe, T. / Hofmann, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEXC1069 Germany
German Research FoundationDIP Programme (LU 315/17-1) Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: His-Ligation to the [4Fe-4S] Subcluster Tunes the Catalytic Bias of [FeFe] Hydrogenase.
Authors: Rodriguez-Macia, P. / Kertess, L. / Burnik, J. / Birrell, J.A. / Hofmann, E. / Lubitz, W. / Happe, T. / Rudiger, O.
History
DepositionMay 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 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)49,4266
Polymers48,9131
Non-polymers5135
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-50 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.730, 70.730, 155.900
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-917-

HOH

21A-963-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48912.727 Da / Num. of mol.: 1 / Mutation: C377H
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) / Variant (production host): DiscR / References: UniProt: Q9FYU1, 1.18.99.1

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Non-polymers , 5 types, 378 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 46.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 12% PEG 4000, 0.6 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→19.905 Å / Num. obs: 80746 / % possible obs: 99.9 % / Redundancy: 9.975 % / Biso Wilson estimate: 29.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.128 / Χ2: 0.958 / Net I/σ(I): 11.6 / Num. measured all: 805470 / Scaling rejects: 34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8510.0982.0081.2460163595959580.4772.116100
1.85-1.910.011.6651.5558168581258110.5491.756100
1.9-1.959.8731.3471.9856195569256920.6761.422100
1.95-2.019.9251.022.7454734551655150.7811.077100
2.01-2.089.6910.8063.5152101537953760.8790.85299.9
2.08-2.158.9670.5824.746037514251340.9280.61899.8
2.15-2.2310.1430.4826.0650574498649860.9550.509100
2.23-2.3210.0960.3627.7247734472847280.9760.382100
2.32-2.4310.0680.2829.4946835465246520.9830.297100
2.43-2.5510.0470.22711.1843985437843780.9870.239100
2.55-2.689.7530.17712.9840594416741620.9920.18799.9
2.68-2.859.7730.12916.4938800398039700.9940.13699.7
2.85-3.0410.7260.10620.2139709370237020.9970.111100
3.04-3.2910.6090.08424.0236622345234520.9980.089100
3.29-3.610.3680.0728.0633095319231920.9980.074100
3.6-4.029.2610.06328.5426282284428380.9980.06799.8
4.02-4.6510.5650.05833.1426899254725460.9990.061100
4.65-5.6910.5150.05833.4122618215121510.9980.061100
5.69-8.059.3680.05832.6415466165616510.9980.06199.7
8.05-19.90510.3980.05838.8788599118520.9970.06193.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.905 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 4056 5.02 %
Rwork0.1694 76685 -
obs0.1708 80741 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.86 Å2 / Biso mean: 40.831 Å2 / Biso min: 19.97 Å2
Refinement stepCycle: final / Resolution: 1.8→19.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 15 373 3464
Biso mean--30.07 44.42 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053161
X-RAY DIFFRACTIONf_angle_d0.9614285
X-RAY DIFFRACTIONf_chiral_restr0.036478
X-RAY DIFFRACTIONf_plane_restr0.004555
X-RAY DIFFRACTIONf_dihedral_angle_d13.5021179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.82120.32561380.297426472785
1.8212-1.84340.3481320.282326032735
1.8434-1.86670.30911440.283226882832
1.8667-1.89120.27531440.277526172761
1.8912-1.91710.30941400.273326692809
1.9171-1.94450.30871400.279826492789
1.9445-1.97350.32451320.267926572789
1.9735-2.00430.27011400.250126042744
2.0043-2.03710.2571340.236926692803
2.0371-2.07220.24661440.23126152759
2.0722-2.10990.23041380.205126742812
2.1099-2.15040.23011360.190226872823
2.1504-2.19420.21791360.193526182754
2.1942-2.24190.19831380.182426022740
2.2419-2.2940.25181280.17226642792
2.294-2.35120.20461540.156426762830
2.3512-2.41470.19191420.156226382780
2.4147-2.48560.20841360.157126322768
2.4856-2.56570.18111360.158926442780
2.5657-2.65720.20851420.166226302772
2.6572-2.76330.23681360.161726432779
2.7633-2.88870.18671480.172526182766
2.8887-3.04050.21751380.159826612799
3.0405-3.23030.18951340.157526852819
3.2303-3.47850.16631460.144926272773
3.4785-3.82630.21121420.141626522794
3.8263-4.37480.1531460.127426492795
4.3748-5.49260.14491490.133526382787
5.4926-19.90610.15241430.183526292772

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