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- PDB-5o4h: HcgC from Methanococcus maripaludis cocrystallized with SAM and p... -

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Basic information

Entry
Database: PDB / ID: 5o4h
TitleHcgC from Methanococcus maripaludis cocrystallized with SAM and pyridinol
ComponentsHcgC
KeywordsTRANSFERASE / methyltransferases / biosynthesis / protein structures / enzyme catalysis / mutagenesis / [Fe]-hydrogenase / pyridinol / Hmd
Function / homologyFeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC / ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWagner, T. / Bai, L. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC.
Authors: Bai, L. / Wagner, T. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.
History
DepositionMay 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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: HcgC
B: HcgC
C: HcgC
D: HcgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,52423
Polymers123,7704
Non-polymers3,75419
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-123 kcal/mol
Surface area41240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.168, 77.736, 100.991
Angle α, β, γ (deg.)90.00, 110.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
HcgC


Mass: 30942.623 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A his-tagged has been placed in the C-terminal of the construct
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Cell line: / / Gene: MMP1498 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6LX54

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Non-polymers , 6 types, 718 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.17 Å3/Da / Density % sol: 43.4 % / Description: Thick transparent hexagonal brick
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 5 mg/ml of pure HcgC containing 2 mM SAM and 2 mM pyridinol was used and mixed at a ratio of 1 ul with 1 ul of precipitant composed of 50% v/v PEG 400, 100 mM NaAcetate pH 4.5 and 200 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.75→47.85 Å / Num. obs: 106203 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.041 / Net I/σ(I): 9.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15490 / CC1/2: 0.421 / Rpim(I) all: 0.331 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D4V

5d4v


Resolution: 1.75→47.85 Å / Cor.coef. Fo:Fc: 0.9603 / Cor.coef. Fo:Fc free: 0.9512 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 5307 5 %RANDOM
Rwork0.1675 ---
obs0.1688 106177 99.6 %-
Displacement parametersBiso mean: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.4782 Å20 Å20.8315 Å2
2--0.5191 Å20 Å2
3---2.9591 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: 1 / Resolution: 1.75→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16869 0 200 699 17768
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117269HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2131430HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4045SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2365HARMONIC20
X-RAY DIFFRACTIONt_it17269HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.47
X-RAY DIFFRACTIONt_other_torsion13.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1177SEMIHARMONIC5
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_contact19229SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2638 409 5.25 %
Rwork0.2254 7388 -
all0.2274 7797 -
obs--99.6 %
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)
10.71280.06360.27151.10950.19711.11570.00560.090.0192-0.16730.03020.0052-0.03330.0332-0.0358-0.037-0.03160.0196-0.04450.0295-0.058832.54782.6335-13.8605
20.55820.14960.22660.9658-0.03871.5873-0.0226-0.02-0.06050.1875-0.032-0.2034-0.16050.12320.0547-0.0501-0.0318-0.0358-0.03190.0279-0.027142.563110.428723.2604
30.68950.15740.97441.05820.45181.6311-0.0617-0.08940.0838-0.0718-0.070.324-0.0448-0.16930.1317-0.1121-0.0009-0.027-0.0813-0.01320.0786-0.0026-2.4137-1.628
40.6401-0.33040.33370.4673-0.06462.1783-0.043-0.1173-0.09480.1904-0.02440.11490.2457-0.16850.06740.0085-0.01840.0808-0.08-0.0045-0.029916.4145-11.247632.2562
50.1535-0.0923-0.10650.25370.4058-0.0594-0.00060.0006-0.0021-0.0023-0.00160.00290.00250.0020.00220.0024-0.0014-0.00170.0015-0.0052-0.004433.86979.7545.2139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ H|* }

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