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- PDB-6hae: Crystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus ae... -

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Basic information

Entry
Database: PDB / ID: 6hae
TitleCrystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus aeolicus in complex with FeGP cofactor and methenyl-tetrahydromethanopterin (close form B)
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 / 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
Chem-E4M / iron-guanylyl pyridinol cofactor / : / THIOCYANATE ION / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanococcus aeolicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 ...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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5,10-methenyltetrahydromethanopterin hydrogenase
K: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,26032
Polymers73,5692
Non-polymers4,69130
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homolog proteins (PDB 4JJF) are known to make dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-182 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.015, 156.480, 53.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AK

#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.: 2 / 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)
Strain: ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3 / 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 , 9 types, 622 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-E4M / 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol


Mass: 787.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H44N6O16P
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-FE9 / iron-guanylyl pyridinol cofactor


Mass: 686.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23FeN6O13PS
#9: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 46.22 % / Description: Transparent plate-shape crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization of [Fe]-hydrogenase-methenyl-H4MPT+ complex was performed in an anaerobic tent with gas phase 100%N2 at room temperature under dark condition. The reconstituted [Fe]- ...Details: Crystallization of [Fe]-hydrogenase-methenyl-H4MPT+ complex was performed in an anaerobic tent with gas phase 100%N2 at room temperature under dark condition. The reconstituted [Fe]-hydrogenase holoenzyme (50 mg/ml) was mixed with 10-mM methenyl-H4MPT+, both of which contained 10-mM MOPS/KOH pH 7.0. The final concentrations of [Fe]-hydrogenase and methenyl-H4MPT+ were 24 mg/ml and 3 mM, respectively. After incubating the mixture in this tent under dark condition for 5 min, the enzyme solution was centrifuged using MiniSpin-plus (Eppendorf) at 8000 rpm for 5 min by using centrifugal filters made of polyvinylidene fluoride (PVDF, Millipore). The crystallization solution contained 20 % w/v polyethylene glycol 3350, 200 mM sodium thiocyanate and 3% w/v 1,5-diaminopentane dihydrochloride with a ratio of protein mixture and crystallization reservoir of 0.7 ul / 0.7 ul drops (in 96 well-plates).
PH range: /
Temp details: The protein was crystallized at room temperature with about 3-4 degree of temperature variation

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 1.85→44.56 Å / Num. obs: 56771 / % possible obs: 97.4 % / Redundancy: 6 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.055 / Rrim(I) all: 0.135 / Net I/σ(I): 8.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.133 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6994 / CC1/2: 0.323 / Rpim(I) all: 0.627 / Rrim(I) all: 1.301 / % possible all: 85

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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: 6HAC

6hac


Resolution: 1.85→44.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2804 4.94 %RANDOM
Rwork0.161 ---
obs0.163 56710 97.1 %-
Displacement parametersBiso mean: 28.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.8163 Å20 Å20 Å2
2---1.9962 Å20 Å2
3----1.8201 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.85→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 264 592 5988
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110794HARMONIC6
X-RAY DIFFRACTIONt_angle_deg1.1119596HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d2446SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1657HARMONIC20
X-RAY DIFFRACTIONt_it10794HARMONIC20
X-RAY DIFFRACTIONt_nbd19SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion12.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion758SEMIHARMONIC5
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_contact12123SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2703 164 4.92 %
Rwork0.2198 3172 -
all0.2223 3336 -
obs--79.3 %

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