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- PDB-5ok4: Crystal structure of native [Fe]-hydrogenase Hmd from Methanother... -

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Basic information

Entry
Database: PDB / ID: 5ok4
TitleCrystal structure of native [Fe]-hydrogenase Hmd from Methanothermobacter marburgensis inactivated by O2.
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / [Fe]-hydrogenase / Fe-Guanylylpyridinol cofactor / H2 / hydrogenase / methanogenesis / methenyl-tetrahydromethanopterin / methylene-tetrahydromethanopterin / hydrogenation / O2 / inactivation
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-FEG / 5,10-methenyltetrahydromethanopterin hydrogenase
Similarity search - Component
Biological speciesMethanothermobacter marburgensis str. Marburg (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsWagner, T. / Huang, G. / Bill, E. / Ermler, U. / Ataka, K. / Shima, S.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates.
Authors: Huang, G. / Wagner, T. / Ermler, U. / Bill, E. / Ataka, K. / Shima, S.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_atom_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4956
Polymers37,6931
Non-polymers8025
Water9,296516
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)230,97036
Polymers226,1586
Non-polymers4,81230
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area39050 Å2
ΔGint-438 kcal/mol
Surface area70370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.418, 127.418, 141.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-403-

FE

21A-766-

HOH

31A-871-

HOH

41A-1002-

HOH

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Components

#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: 37692.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis str. Marburg (archaea)
Cell line: / / Organ: / / Tissue: /
References: UniProt: P32440, 5,10-methenyltetrahydromethanopterin hydrogenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-FEG / 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine


Mass: 542.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N6O11P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.93 Å3/Da / Density % sol: 58.04 %
Description: Transparent cube shape of about 100x100 micrometer.
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1-ml mixture containing 120 mM potassium phosphate pH 6.0, 1 mM EDTA, 26 uM (1 mg/ml) [Fe]-hydrogenase and 26 uM methylene-H4MPT was incubated in 5-ml amber vials with rubber stoppers under ...Details: 1-ml mixture containing 120 mM potassium phosphate pH 6.0, 1 mM EDTA, 26 uM (1 mg/ml) [Fe]-hydrogenase and 26 uM methylene-H4MPT was incubated in 5-ml amber vials with rubber stoppers under a gas mixture of N2/O2/H2 (70%/20%/10%) at 40 degree Celsius for 1 h. The inactivated enzyme was concentrated to 25 mg/ml using a 30 kDa centrifugal filter (Millipore). 0.7-ul of 25 mg/ml O2-inactivated [Fe]-hydrogenase was mixed with 0.7 ul of reservoir solution of 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, and 200 mM LiSO4. The best diffracting crystal was obtained in one month. Prior to freezing the crystal was soaked for 3 seconds in 2 M (NH4)2SO4, 100 mM Tris/HCl, pH 7.0, 200 mM LiSO4 and 30% glycerol v/v.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.29→47.07 Å / Num. obs: 110077 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Net I/σ(I): 19.6
Reflection shellResolution: 1.29→1.36 Å / Redundancy: 8 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 15981 / CC1/2: 0.638 / Rpim(I) all: 0.423 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJF

2jjf


Resolution: 1.29→43.474 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.61
RfactorNum. reflection% reflection
Rfree0.1471 5448 4.95 %
Rwork0.127 --
obs0.128 110053 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 1.29→43.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 46 516 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012867
X-RAY DIFFRACTIONf_angle_d1.1943921
X-RAY DIFFRACTIONf_dihedral_angle_d24.2651098
X-RAY DIFFRACTIONf_chiral_restr0.086442
X-RAY DIFFRACTIONf_plane_restr0.009513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30470.21861720.23493487X-RAY DIFFRACTION100
1.3047-1.320.27761810.24343445X-RAY DIFFRACTION100
1.32-1.33610.25441860.21993438X-RAY DIFFRACTION100
1.3361-1.3530.24251810.2083486X-RAY DIFFRACTION100
1.353-1.37080.23211530.19873484X-RAY DIFFRACTION100
1.3708-1.38960.21861910.18943470X-RAY DIFFRACTION100
1.3896-1.40950.19961730.1723481X-RAY DIFFRACTION100
1.4095-1.43050.18131970.15893461X-RAY DIFFRACTION100
1.4305-1.45290.1681720.14533454X-RAY DIFFRACTION100
1.4529-1.47670.19021930.13683439X-RAY DIFFRACTION100
1.4767-1.50210.15711780.12833480X-RAY DIFFRACTION100
1.5021-1.52950.15761710.12383486X-RAY DIFFRACTION100
1.5295-1.55890.14111930.11663462X-RAY DIFFRACTION100
1.5589-1.59070.1481750.11053502X-RAY DIFFRACTION100
1.5907-1.62530.14811720.10843456X-RAY DIFFRACTION100
1.6253-1.66310.13381740.10573486X-RAY DIFFRACTION100
1.6631-1.70470.12391810.10283477X-RAY DIFFRACTION100
1.7047-1.75080.14781960.10273465X-RAY DIFFRACTION100
1.7508-1.80230.12771870.10183463X-RAY DIFFRACTION100
1.8023-1.86050.12991850.10593484X-RAY DIFFRACTION100
1.8605-1.9270.13011900.11883476X-RAY DIFFRACTION100
1.927-2.00410.14381810.11253478X-RAY DIFFRACTION100
2.0041-2.09530.12881840.11113503X-RAY DIFFRACTION100
2.0953-2.20580.13831890.11083488X-RAY DIFFRACTION100
2.2058-2.3440.12991640.11273521X-RAY DIFFRACTION100
2.344-2.5250.12111740.11623492X-RAY DIFFRACTION100
2.525-2.7790.15421940.12263517X-RAY DIFFRACTION100
2.779-3.1810.12571670.13133538X-RAY DIFFRACTION100
3.181-4.00730.14341890.12613552X-RAY DIFFRACTION100
4.0073-43.49890.15762050.14123634X-RAY DIFFRACTION100

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