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- PDB-6yka: Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and ... -

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Basic information

Entry
Database: PDB / ID: 6yka
TitleAsymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution
Components5,10-methenyltetrahydromethanopterin hydrogenase
KeywordsOXIDOREDUCTASE / [Fe]-hydrogenase / FeGP cofactor / guanylylpyridinol / asymmetry / conformational changes / GMP
Function / homologyiron-guanylyl pyridinol cofactor / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMethanolacinia paynteri G-2000 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWagner, T. / Huang, G. / Arriaza-Gallardo, F.J. / Shima, S.
Funding support Germany, China, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)Iron sulfur for life SH87/1-1 Germany
Ministry of Education (MoE, China)China Scholarship Council China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.
Authors: Huang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
History
DepositionApr 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,08214
Polymers74,4462
Non-polymers1,63512
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-58 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.481, 79.481, 179.337
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5,10-methenyltetrahydromethanopterin hydrogenase


Mass: 37223.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanolacinia paynteri G-2000 (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: hmd / Organ: /
Details (production host): The DNA synthesized was inserted into the expression vector pET-24b (+) at the NdeI and SalI restriction-enzyme digestion-sites
Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): /
References: 5,10-methenyltetrahydromethanopterin hydrogenase

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Non-polymers , 5 types, 236 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FE9 / iron-guanylyl pyridinol cofactor


Mass: 686.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23FeN6O13PS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.45 % / Description: Transparent prism shape
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml ...Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution under yellow light and incubated under dark conditions. The crystals grew within two weeks in 30% w/v polyethylene glycol 4000, 200-mM lithium sulfate and 100-mM Tris pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience).
PH range: 8.5 / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→68.833 Å / Num. obs: 39181 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 41.7 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Rsym value: 0.059 / Net I/av σ(I): 11.7 / Net I/σ(I): 28.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.1-2.2111.10.7111.156430.7550.2220.7460.711100
2.21-2.35110.531.553280.1660.5550.53100
2.35-2.51110.3342.350160.1050.3510.334100
2.51-2.71110.193446980.060.2020.193100
2.71-2.97110.1226.443330.0380.1280.122100
2.97-3.3210.90.06312.239440.020.0660.063100
3.32-3.8310.80.03719.835000.0120.0390.037100
3.83-4.710.50.02526.129970.0080.0270.025100
4.7-6.6410.20.0232823610.0070.0240.023100
6.64-44.8348.90.01834.113610.0060.0190.01898.5

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJF

4jjf


Resolution: 2.1→39.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.186
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1876 4.79 %RANDOM
Rwork0.195 ---
obs0.197 39126 99.9 %-
Displacement parametersBiso max: 220.76 Å2 / Biso mean: 61.86 Å2 / Biso min: 15.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.4312 Å20 Å20 Å2
2---0.4312 Å20 Å2
3---0.8623 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.1→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 103 224 5523
Biso mean--70.1 52.57 -
Num. residues----682
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2446SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1634HARMONIC20
X-RAY DIFFRACTIONt_it10851HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion750SEMIHARMONIC5
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_contact12288SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10851HARMONIC40.008
X-RAY DIFFRACTIONt_angle_deg19767HARMONIC41.01
X-RAY DIFFRACTIONt_omega_torsion1.66
X-RAY DIFFRACTIONt_other_torsion14.57
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2505 125 4.36 %
Rwork0.2136 2739 -
all0.2152 2864 -
obs--100 %
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)
11.6552-0.28740.97630.6833-0.53344.3107-0.10180.44330.1196-0.0084-0.1082-0.23020.20380.74310.21-0.2230.0087-0.0311-0.11170.1005-0.0598-46.092111.8257-7.6979
20.8782-0.71260.48651.9586-1.50913.9268-0.2128-0.3902-0.03320.37580.42460.166-0.1472-0.6247-0.2117-0.18970.1048-0.0309-0.0320.0609-0.1305-58.97376.793331.6297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 342
2X-RAY DIFFRACTION2{ B|* }B2 - 342

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