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- PDB-6hux: HmdII from Methanocaldococcus jannaschii reconstitued with Fe-gua... -

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Basic information

Entry
Database: PDB / ID: 6hux
TitleHmdII from Methanocaldococcus jannaschii reconstitued with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydromethanopterin at 2.5 A resolution
ComponentsH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
KeywordsOXIDOREDUCTASE / Hydrogenase / H2-activation / Lateral gene-transfer / cofactor biosynthesis / tetrahydromethanopterin / paralog / methanogen / metalloenzyme
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein / 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) ...H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein / 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
ACETATE ION / Chem-E4M / iron-guanylyl pyridinol cofactor / H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWatanabe, T. / Wagner, T. / Huang, G. / Kahnt, J. / Ataka, K. / Ermler, U. / Shima, S.
Funding support Germany, China, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
Ministry of Education (China) China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: The Bacterial [Fe]-Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates.
Authors: Watanabe, T. / Wagner, T. / Huang, G. / Kahnt, J. / Ataka, K. / Ermler, U. / Shima, S.
History
DepositionOct 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,61125
Polymers40,6641
Non-polymers2,94724
Water95553
1
A: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
hetero molecules

A: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,22150
Polymers81,3282
Non-polymers5,89448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_567x-y+2/3,-y+4/3,-z+7/31
Buried area19050 Å2
ΔGint-323 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.281, 124.281, 150.086
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-416-

SO4

21A-416-

SO4

31A-514-

HOH

41A-553-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338


Mass: 40663.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: MJ1338 / Organ: / / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): /
References: UniProt: Q58734, 5,10-methenyltetrahydromethanopterin hydrogenase

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Non-polymers , 9 types, 77 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FE9 / iron-guanylyl pyridinol cofactor


Mass: 686.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23FeN6O13PS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.75 Å3/Da / Density % sol: 55.25 % / Description: transparent flower shape
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: HmdII from Methanocaldococcus jannaschii reconstituted with Fe-guanylylpyridinol cofactor was cocrystallized with methenyl-tetrahydromethanopterin using the sitting drop vapor diffusion ...Details: HmdII from Methanocaldococcus jannaschii reconstituted with Fe-guanylylpyridinol cofactor was cocrystallized with methenyl-tetrahydromethanopterin using the sitting drop vapor diffusion method under N2/H2 (95%/5%) in red light condition. 20 mg/ml of reconstituted enzyme in 25 mM Tris pH 7.5, 5% glycerol, 150 mM NaCl, 2 mM DTT and 3 mM methenyl-tetrahydromethanopterin was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) with a ratio of 0.7 ul of protein and 0.7 ul of reservoir solution. After several weeks, crystals appeared in 2 M LiSO4, 100 mM Sodium acetate pH 5.5, 100 mM MgSO4 and 5% v/v PEG 400. jHmdII crystal was cryoprotected in its mother liquor supplemented with 30% ethylene glycol before freezing in liquid nitrogen.
Temp details: The temperature fluctuation was +/- 1 degree

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.5→43.73 Å / Num. obs: 15610 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 64.85 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.341 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2224 / CC1/2: 0.686 / Rpim(I) all: 0.447 / Rrim(I) all: 1.415 / % possible all: 99.9

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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: 4YT4

4yt4


Resolution: 2.5→38.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.372 / SU Rfree Blow DPI: 0.236
Details: The last refinement cycle was performed with hydrogens in riding position. The hydrogens have been removed from the deposited model.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 739 4.74 %RANDOM
Rwork0.165 ---
obs0.168 15602 99.9 %-
Displacement parametersBiso mean: 64.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.8028 Å20 Å20 Å2
2--2.8028 Å20 Å2
3----5.6056 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.5→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 157 53 3000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085932HARMONIC5
X-RAY DIFFRACTIONt_angle_deg0.9910781HARMONIC5
X-RAY DIFFRACTIONt_dihedral_angle_d1354SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes912HARMONIC20
X-RAY DIFFRACTIONt_it5932HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion15.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion398SEMIHARMONIC5
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_contact6570SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3038 135 4.88 %
Rwork0.2078 2633 -
all0.2125 2768 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.21680.47-1.72722.23380.63551.0907-0.00750.09730.29580.07440.1759-0.4598-0.09430.1063-0.16840.3406-0.0239-0.06580.43390.00690.5584-27.8885101.3027183.75
23.2452-0.7766-0.68992.2617-0.16583.0057-0.2845-0.08280.75540.28070.0956-0.6346-0.40010.25680.18890.4326-0.0049-0.13630.34480.01590.6662-31.2783107.8108189.045
32.7008-0.94680.36092.88870.06241.08520.01740.36460.2473-0.0969-0.1040.0039-0.1214-0.06450.08660.26920.0411-0.0470.36930.02640.3451-42.902697.6746177.59
40.80970.42480.27453.61210.871.2615-0.04260.1179-0.0315-0.2378-0.09740.03180.0227-0.00480.14010.2376-0.01340.0120.3959-0.00230.2998-34.994868.2809171.542
52.7431-0.48730.09473.22880.86842.0376-0.0282-0.3893-0.3980.2397-0.0908-0.1490.10140.04460.1190.316-0.02640.01350.42420.00510.3335-34.691464.4043178.461
6-0.31240.13970.09270.59470.84780-0.0481-0.708-0.50760.6508-0.07740.37090.2508-0.01420.12550.56960.04210.08690.7989-0.05810.4966-52.434784.493192.045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|3 - A|42 }
2X-RAY DIFFRACTION2{ A|43 - A|85 }
3X-RAY DIFFRACTION3{ A|86 - A|213 }
4X-RAY DIFFRACTION4{ A|214 - A|270 }
5X-RAY DIFFRACTION5{ A|271 - A|336 }
6X-RAY DIFFRACTION6{ A|337 - A|371 }

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