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- PDB-6ykb: [Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP... -

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Basic information

Entry
Database: PDB / ID: 6ykb
Title[Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP at 1.55-A resolution
Components5,10-methenyltetrahydromethanopterin [Fe]-hydrogenase
KeywordsOXIDOREDUCTASE / [Fe]-hydrogenase / FeGP cofactor / guanylylpyridinol / conformational changes / GMP
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / FORMIC ACID
Function and homology information
Biological speciesMethanolacinia paynteri G-2000 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 [Fe]-hydrogenase
C: 5,10-methenyltetrahydromethanopterin [Fe]-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,63313
Polymers74,4462
Non-polymers1,18711
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-98 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.805, 57.058, 95.125
Angle α, β, γ (deg.)90.000, 91.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5,10-methenyltetrahydromethanopterin [Fe]-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: / / Variant: DSM 2545
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
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.95 % / Description: Large rod shape
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Fe-hydrogenase holoenzyme from Methanolacinia paynteri was crystallized under 95%N2/5%H2 at 8 degree Celsius using a 96-well two-drop MRC crystallization plates. 0.7 ul of 25 mg/ml ...Details: Fe-hydrogenase holoenzyme from Methanolacinia paynteri was crystallized under 95%N2/5%H2 at 8 degree Celsius using a 96-well two-drop MRC crystallization plates. 0.7 ul of 25 mg/ml reconstituted enzyme with an Fe(II)-complex mimicking the FeGP cofactor and GMP (2mM final) was mixed with 0.7-ul reservoir solution under yellow light and incubated under dark conditions. The best crystal appeared within one month in 20% w/v polyethylene glycol 3350 and 200-mM magnesium formate reservoir solution (JBScreen Wizard 3&4 HTS, Jena Bioscience). The cryo protection was performed by adding 30% glycerol final to the crystallization solution.
PH range: 7 / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97972 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: 0.97972 Å / Relative weight: 1
ReflectionResolution: 1.55→95.095 Å / Num. obs: 104812 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Rsym value: 0.068 / Net I/av σ(I): 8.8 / Net I/σ(I): 12.6
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
1.55-1.633.70.3532.2152850.6530.2130.4130.35399.7
1.63-1.733.70.2832.7145150.170.3310.28399.7
1.73-1.853.70.2153.6135630.1290.2510.21599.7
1.85-23.70.1445.3126540.0870.1690.14499.5
2-2.193.70.0928.3116560.0560.1080.09299.3
2.19-2.453.70.07110.6105380.0430.0830.07199.3
2.45-2.833.70.05612.793150.0340.0660.05699.4
2.83-3.473.60.04814.378380.030.0560.04898.7
3.47-4.93.60.03617.861160.0220.0430.03699
4.9-39.9153.60.03218.833320.020.0380.03296.1

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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: 1.55→22.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5065 4.83 %RANDOM
Rwork0.184 ---
obs0.185 104777 99.3 %-
Displacement parametersBiso max: 110.92 Å2 / Biso mean: 22.16 Å2 / Biso min: 3.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.4657 Å20 Å20.4452 Å2
2--2.2687 Å20 Å2
3----4.7344 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.55→22.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 78 640 5915
Biso mean--26.42 29.38 -
Num. residues----682
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2442SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1684HARMONIC20
X-RAY DIFFRACTIONt_it10876HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
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_contact12292SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10876HARMONIC40.01
X-RAY DIFFRACTIONt_angle_deg19813HARMONIC41.1
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion14.27
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2464 350 4.53 %
Rwork0.2119 7372 -
all0.2135 7722 -
obs--99.69 %
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)
10.61890.1524-0.37230.5363-0.43881.19270.0006-0.1233-0.076-0.0169-0.0878-0.05310.02730.24840.0872-0.07350.01030.0038-0.03550.0017-0.020483.0443-10.612141.2078
20.4441-0.17530.17560.8546-0.54710.76380.05270.0530.086-0.1483-0.1217-0.08940.08210.15030.069-0.01250.01490.0245-0.067-0.0014-0.037283.765611.93047.4172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 342
2X-RAY DIFFRACTION2{ C|* }C2 - 342

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