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- PDB-6huz: HmdII from Desulfurobacterium thermolithotrophum reconstituted wi... -

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Basic information

Entry
Database: PDB / ID: 6huz
TitleHmdII from Desulfurobacterium thermolithotrophum reconstituted with Fe-guanylylpyridinol (FeGP) cofactor and co-crystallized with methenyl-tetrahydrofolate form B
ComponentsCoenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
KeywordsOXIDOREDUCTASE / Hydrogenase / H2-activation / Lateral gene-transfer / cofactor biosynthesis / tetrahydromethanopterin / tetrahydrofolate / paralog / sulfur-reducing bacteria / metalloenzyme
Function / homologyH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein / 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 / NAD(P)-binding domain superfamily / iron-guanylyl pyridinol cofactor / 5,10-Methenyltetrahydrofolate / Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
Function and homology information
Biological speciesDesulfurobacterium thermolithotrophum DSM 11699 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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: Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4529
Polymers40,9941
Non-polymers1,4588
Water5,062281
1
A: Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
hetero molecules

A: Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,90418
Polymers81,9882
Non-polymers2,91616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area15170 Å2
ΔGint-194 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.200, 132.020, 49.160
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, 1 molecules A

#1: Protein Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase-related protein


Mass: 40994.000 Da / Num. of mol.: 1 / Mutation: wild-type
Source method: isolated from a genetically manipulated source
Details: synthetic gene
Source: (gene. exp.) Desulfurobacterium thermolithotrophum DSM 11699 (bacteria)
Tissue: / / Cell: / / Cell line: / / Gene: Dester_1504 / Organ: / / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / References: UniProt: F0S2B6

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Non-polymers , 6 types, 289 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-GUE / 5,10-Methenyltetrahydrofolate


Mass: 456.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N7O6
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.58 Å3/Da / Density % sol: 52.43 % / Description: Transparent triangular shape
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: HmdII from Desulfurobacterium thermolithotrophum was reconstituted with the Fe-guanylylpyridinol cofactor from Methanothermobacter marburgensis and co-crystallized with methenyl- ...Details: HmdII from Desulfurobacterium thermolithotrophum was reconstituted with the Fe-guanylylpyridinol cofactor from Methanothermobacter marburgensis and co-crystallized with methenyl-tetrahydrofolate using the sitting drop vapor diffusion method under N2/H2 (95%/5%) in red light condition. The reconstituted holoenzyme was mixed with methenyl-H4F+ at the final concentrations of 1.6 mM. Methenyl-tetrahydrofolate was dissolved in 10% DMSO, and the final concentration of DMSO in the protein solution was 1.6%. 0.7 ul of dHmdII at 21 mg/ml (reconstituted with FeGP and methenyl-H4F+) was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) and 0.7 ul of reservoir solution was mixed. After one month, crystals appeared in 20% PEG 3000 (w/v) and 100 mM Sodium Citrate pH 5.5 (from the kit WIZARD, Jena Bioscience). The crystals were cryoprotected by a soak of few seconds in 20% PEG 3000 (w/v), 100 mM Tri-Sodium Citrate pH 5.5 and 20% glycerol before a flash freeze in liquid nitrogen
Temp details: The temperature was fluctuating by +/- 1 degree

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→49.16 Å / Num. obs: 37060 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5308 / CC1/2: 0.849 / Rpim(I) all: 0.511 / Rrim(I) all: 1.317 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HUY

6huy


Resolution: 1.85→46.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.121
Details: The C-terminal helix 335-347 might be in two different position and only the one with the highest occupancy has been modelled. The final part 350-356 has been traced to fit an extra electron ...Details: The C-terminal helix 335-347 might be in two different position and only the one with the highest occupancy has been modelled. The final part 350-356 has been traced to fit an extra electron density, however it is not excluded that this density corresponds to polyethylene glycol. The hydrogens have been added in riding position for the last refinement cycle and have been omitted in the deposited model.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1812 4.97 %RANDOM
Rwork0.195 ---
obs0.196 36480 98.4 %-
Displacement parametersBiso mean: 44.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.3291 Å20 Å20 Å2
2---0.4571 Å20 Å2
3---1.7863 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.85→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 93 281 3113
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015791HARMONIC5
X-RAY DIFFRACTIONt_angle_deg1.1410552HARMONIC5
X-RAY DIFFRACTIONt_dihedral_angle_d1331SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes864HARMONIC30
X-RAY DIFFRACTIONt_it5791HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.75
X-RAY DIFFRACTIONt_other_torsion15.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
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_contact6579SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3479 145 5.07 %
Rwork0.3009 2717 -
all0.3032 2862 -
obs--95.39 %
Refinement TLS params.Method: refined / Origin x: -31.3793 Å / Origin y: 15.6653 Å / Origin z: 14.6374 Å
111213212223313233
T0.0127 Å2-0.0018 Å2-0.0368 Å2--0.1382 Å2-0.0516 Å2--0.247 Å2
L1.4679 °20.2294 °2-0.0755 °2-1.3605 °2-0.0109 °2--0.269 °2
S-0.0815 Å °-0.1623 Å °0.4523 Å °-0.0848 Å °0.0732 Å °0.0635 Å °-0.0149 Å °-0.0215 Å °0.0082 Å °
Refinement TLS groupSelection details: { A|* }

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