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- PDB-5o4m: Fresh crystals of HcgC from Methanococcus maripaludis cocrystalli... -

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Basic information

Entry
Database: PDB / ID: 5o4m
TitleFresh crystals of HcgC from Methanococcus maripaludis cocrystallized with SAH 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 / 6-carboxy methyl-4-hydroxy-2-pyridinol / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWagner, T. / Bai, L. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.
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)126,86620
Polymers123,7704
Non-polymers3,09616
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-101 kcal/mol
Surface area40500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.875, 83.536, 99.987
Angle α, β, γ (deg.)90.00, 109.54, 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: / / Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Tissue: / / Cell: / / Cell line: / / Gene: MMP1498 / Organ: / / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6LX54

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Non-polymers , 5 types, 538 molecules

#2: Chemical
ChemComp-SAH / 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-9KH / 6-carboxy methyl-4-hydroxy-2-pyridinol


Mass: 183.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H9NO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.29 Å3/Da / Density % sol: 46.3 % / Description: Thick transparent hexagonal brick
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The drop consists of 1 ul of enzyme solution containing ~5 mg/ml HcgC, 2 mM pyridinol (dissolved in 100% DMSO) and 2 mM SAH mixed with 1 ul of the reservoir solution : 100 mM HEPES/NaOH pH 7. ...Details: The drop consists of 1 ul of enzyme solution containing ~5 mg/ml HcgC, 2 mM pyridinol (dissolved in 100% DMSO) and 2 mM SAH mixed with 1 ul of the reservoir solution : 100 mM HEPES/NaOH pH 7.5, 0.1 M NaCl, and 30% 2-Methyl-2,4-pentanediol. After only 4 days the crystals were immediately fished and frozen in liquid nitrogen for synchrotron radiation.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.1→47.11 Å / Num. obs: 63739 / % possible obs: 97.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 40.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9372 / CC1/2: 0.804 / Rpim(I) all: 0.412 / % possible all: 98.8

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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: 5O4H

5o4h


Resolution: 2.1→46.68 Å / Cor.coef. Fo:Fc: 0.9475 / Cor.coef. Fo:Fc free: 0.9206 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 3141 4.93 %RANDOM
Rwork0.2022 ---
obs0.2037 63705 97.75 %-
Displacement parametersBiso mean: 56.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.3751 Å20 Å20.8339 Å2
2---1.1305 Å20 Å2
3----0.2446 Å2
Refine analyzeLuzzati coordinate error obs: 0.368 Å
Refinement stepCycle: 1 / Resolution: 2.1→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16861 0 208 522 17591
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117274HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1931386HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4020SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes224HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2348HARMONIC20
X-RAY DIFFRACTIONt_it17274HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.32
X-RAY DIFFRACTIONt_other_torsion14.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1179SEMIHARMONIC5
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_contact18916SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2702 246 5.22 %
Rwork0.2371 4464 -
all0.2389 4710 -
obs--97.75 %
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)
10.56190.22570.41491.58450.03821.5497-0.08890.09480.0326-0.29410.14030.00140.01270.0169-0.05140.0244-0.02170.1032-0.03210.014-0.146132.63672.7625-14.065
20.45620.11070.49630.9711-0.00421.8619-0.06460.01430.07590.4770.0439-0.106-0.18010.01850.02070.18260.0436-0.0025-0.077-0.0195-0.173442.116412.249321.8558
30.65010.38070.45321.1238-1.26571.0882-0.14990.02330.15720.00870.45680.46780.0966-0.5199-0.3069-0.2296-0.00360.06610.2850.16-0.06950.1003-3.8014-1.2744
40.49250.29780.26690.9141-0.3882.21750.0063-0.0721-0.05160.47050.18750.30150.0288-0.3048-0.19380.10970.11130.2360.00560.0606-0.188517.763-11.951932.0378
5-0.35461.38920.43670-0.61610.3546-0.00010.00010.00490.01360.0002-0.0054-0.0107-0.0033-0.0001-0.0155-0.01180.0026-0.02810.003-0.014828.57762.412317.796
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{ F|* }

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