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

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Entry
Database: PDB / ID: 6hav
TitleCrystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus aeolicus in complex with FeGP and methenyl-tetrahydromethanopterin (close form A) at 1.06 A resolution
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / [Fe]-hydrogenase / catalytic cycle / conformational rearrangement / Fe-guanylylpyridinol cofactor / methanogenesis / hydride-transfer / tetrahydromethanopterin / C1-metabolism / atomic resolution
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 / HMD N-terminal domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...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 / HMD N-terminal domain / 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: 1.06 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 8, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,93913
Polymers36,7851
Non-polymers2,15512
Water9,098505
1
A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules

A: 5,10-methenyltetrahydromethanopterin hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,87926
Polymers73,5692
Non-polymers4,30924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12560 Å2
ΔGint-152 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.648, 66.246, 167.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-989-

HOH

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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 , 6 types, 517 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#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


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#6: 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.: 1 / Source method: obtained synthetically / Formula: C31H44N6O16P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.17 % / Description: Large orthorhombic rod
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization of [Fe]-hydrogenase-methenyl-H4MPT+ complex was performed in the 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 the 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 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 and 200 mM sodium thiocyanate with a ratio of protein mixture and crystallization reservoir of 2 ul / 2 ul drops spotted on a 24 well Junior Clover plate. The crystal was soaked for a couple of seconds in 20% w/v polyethylene glycol 3350, 20% v/v glycerol and 200 mM sodium thiocyanate before freezing in liquid nitrogen.
PH range: /
Temp details: Protein was crystallized at room temperature with + / - 4 degree

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.06→46.98 Å / Num. obs: 156432 / % possible obs: 93.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 1.06→1.12 Å / Redundancy: 4 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 18054 / CC1/2: 0.672 / Rpim(I) all: 0.542 / Rrim(I) all: 1.129 / % possible all: 74.8

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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: 6HAC

6hac


Resolution: 1.06→45.24 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 12.41
RfactorNum. reflection% reflection
Rfree0.1336 7742 4.96 %
Rwork0.118 --
obs0.1187 156000 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.1 Å2
Refinement stepCycle: LAST / Resolution: 1.06→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 136 505 3208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113010
X-RAY DIFFRACTIONf_angle_d1.4254144
X-RAY DIFFRACTIONf_dihedral_angle_d21.4571222
X-RAY DIFFRACTIONf_chiral_restr0.097476
X-RAY DIFFRACTIONf_plane_restr0.01532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.0720.28171740.28783306X-RAY DIFFRACTION63
1.072-1.08470.43321750.35793345X-RAY DIFFRACTION64
1.0847-1.09790.30162300.29973756X-RAY DIFFRACTION72
1.0979-1.11180.22442030.21274492X-RAY DIFFRACTION85
1.1118-1.12640.21822480.19024790X-RAY DIFFRACTION91
1.1264-1.14180.19142390.16594781X-RAY DIFFRACTION90
1.1418-1.15820.15952350.15474782X-RAY DIFFRACTION91
1.1582-1.17550.15242430.13974895X-RAY DIFFRACTION92
1.1755-1.19380.14752470.12844862X-RAY DIFFRACTION93
1.1938-1.21340.15022250.12324954X-RAY DIFFRACTION94
1.2134-1.23430.14742770.12425057X-RAY DIFFRACTION95
1.2343-1.25680.12812990.10584951X-RAY DIFFRACTION96
1.2568-1.28090.12452520.15094X-RAY DIFFRACTION96
1.2809-1.30710.13662480.09645124X-RAY DIFFRACTION96
1.3071-1.33550.11312910.09935072X-RAY DIFFRACTION97
1.3355-1.36660.11962800.09695102X-RAY DIFFRACTION98
1.3666-1.40080.13092300.09715209X-RAY DIFFRACTION98
1.4008-1.43860.11932780.09475176X-RAY DIFFRACTION98
1.4386-1.4810.11173000.09225150X-RAY DIFFRACTION98
1.481-1.52880.11452550.09255207X-RAY DIFFRACTION98
1.5288-1.58340.1222500.08965251X-RAY DIFFRACTION98
1.5834-1.64680.1192840.09355199X-RAY DIFFRACTION99
1.6468-1.72180.11172910.09835237X-RAY DIFFRACTION99
1.7218-1.81250.11612760.10465284X-RAY DIFFRACTION99
1.8125-1.92610.12033120.10885196X-RAY DIFFRACTION99
1.9261-2.07480.11152680.1125333X-RAY DIFFRACTION99
2.0748-2.28360.12352770.10775338X-RAY DIFFRACTION99
2.2836-2.6140.13262850.11775340X-RAY DIFFRACTION99
2.614-3.29330.13373080.12295372X-RAY DIFFRACTION100
3.2933-45.28160.15072620.13425603X-RAY DIFFRACTION100

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