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- PDB-6hac: Crystal structure of [Fe]-hydrogenase (Hmd) holoenzyme from Metha... -

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Basic information

Entry
Database: PDB / ID: 6hac
TitleCrystal structure of [Fe]-hydrogenase (Hmd) holoenzyme from Methanococcus aeolicus (open form)
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / [Fe]-hydrogenase / catalytic cycle / conformational rearrangement / Fe-guanylylpyridinol cofactor / methanogenesis / hydride-transfer / tetrahydromethanopterin / C1-metabolism
Function / homology
Function and homology information


5,10-methenyltetrahydromethanopterin hydrogenase / N5,N10-methenyltetrahydromethanopterin hydrogenase activity / methanogenesis, from carbon dioxide / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / one-carbon metabolic process
Similarity search - Function
5,10-methenyltetrahydromethanopterin hydrogenase / Hmd, C-terminal helical subdomain / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...5,10-methenyltetrahydromethanopterin hydrogenase / Hmd, C-terminal helical subdomain / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
iron-guanylyl pyridinol cofactor / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanococcus aeolicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, G. / Wagner, T. / Wodrich, M.D. / Ataka, K. / Bill, E. / Ermler, U. / Hu, X. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Catal / Year: 2019
Title: The atomic-resolution crystal structure of activated [Fe]-hydrogenase
Authors: Huang, G. / Wagner, T. / Wodrich, M.D. / Ataka, K. / Bill, E. / Ermler, U. / Hu, X. / Shima, S.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 17, 2024Group: 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: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9166
Polymers36,7851
Non-polymers1,1325
Water1,928107
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules

A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,83312
Polymers73,5692
Non-polymers2,26410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x,-y-1/2,-z-3/41
Buried area9550 Å2
ΔGint-97 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.985, 136.985, 117.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5,10-methenyltetrahydromethanopterin hydrogenase / H(2)-dependent methylene-H(4)MPT dehydrogenase / H(2)-forming N(5) / N(10)- ...H(2)-dependent methylene-H(4)MPT dehydrogenase / H(2)-forming N(5) / N(10)-methylenetetrahydromethanopterin dehydrogenase / N(5) / N(10)-methenyltetrahydromethanopterin hydrogenase


Mass: 36784.562 Da / Num. of mol.: 1 / Mutation: wild-type
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3) (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: hmd, Maeo_1025 / Organ: / / Variant: / / Plasmid: pET-24b+ / Details (production host): / / Cell (production host): / / Cell line (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): /
References: UniProt: A6UVT1, 5,10-methenyltetrahydromethanopterin hydrogenase

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Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-FE9 / iron-guanylyl pyridinol cofactor


Mass: 686.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23FeN6O13PS
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.74 Å3/Da / Density % sol: 67.17 % / Description: Transparent diamond shape
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: The reconstituted [Fe]-hydrogenase holoenzyme from M. aeolicus was crystallized in the anaerobic tent with gas phase 95%N2/5%H2 using 96-well 2-drop MRC Crystallization Plates (Molecular ...Details: The reconstituted [Fe]-hydrogenase holoenzyme from M. aeolicus was crystallized in the anaerobic tent with gas phase 95%N2/5%H2 using 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK). For the initial screening, 0.7-ul of 24 mg/ml reconstituted [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of crystallization kits under yellow light and incubated under the dark condition. The best diffracting crystal was obtained in one month in the crystallization reservoir solution containing 20% w/v polyethylene glycol 3350, 100-mM tri-sodium citrate pH 4.0 and 200-mM tri-sodium citrate.
PH range: /
Temp details: Temperature variation was +/- 1 during crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→48.43 Å / Num. obs: 25078 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 39.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.043 / Rrim(I) all: 0.161 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14 % / Rmerge(I) obs: 1.023 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3607 / CC1/2: 0.602 / Rpim(I) all: 0.281 / Rrim(I) all: 1.061 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJF

4jjf


Resolution: 2.3→26.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1229 4.91 %RANDOM
Rwork0.171 ---
obs0.172 25043 100 %-
Displacement parametersBiso mean: 43.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.5933 Å20 Å20 Å2
2--2.5933 Å20 Å2
3----5.1866 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.3→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 66 107 2740
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095343HARMONIC5
X-RAY DIFFRACTIONt_angle_deg1.119741HARMONIC5
X-RAY DIFFRACTIONt_dihedral_angle_d1197SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes815HARMONIC20
X-RAY DIFFRACTIONt_it5343HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.27
X-RAY DIFFRACTIONt_other_torsion13.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion367SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6166SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2634 144 5.15 %
Rwork0.224 2651 -
all0.226 2795 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -2.1917 Å / Origin y: -41.5428 Å / Origin z: -22.9285 Å
111213212223313233
T-0.1389 Å2-0.028 Å2-0.0291 Å2--0.1328 Å20.0533 Å2--0.1276 Å2
L0.3834 °20.1552 °2-0.0942 °2-0.9126 °2-0.5705 °2--1.0151 °2
S0.0442 Å °-0.0642 Å °0.0607 Å °0.1333 Å °-0.1338 Å °-0.1215 Å °-0.1161 Å °0.0397 Å °0.0896 Å °
Refinement TLS groupSelection details: { A|* }

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