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- PDB-5o4n: Apo HcgC from Methanococcus maripaludis soaked with SAH and pyridinol -

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Basic information

Entry
Database: PDB / ID: 5o4n
TitleApo HcgC from Methanococcus maripaludis soaked 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: 2.05 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)126,94421
Polymers123,7704
Non-polymers3,17417
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-103 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.556, 80.997, 97.808
Angle α, β, γ (deg.)90.00, 108.24, 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: / / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): Star / References: UniProt: Q6LX54

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Non-polymers , 5 types, 487 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-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 / 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 / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.21 Å3/Da / Density % sol: 44.35 % / 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 mixed with 1 ul of the reservoir solution : 100 mM HEPES/NaOH pH 7.5, 0.1 M NaCl, and 30% MPD (2-Methyl-2,4-pentanediol). ...Details: The drop consists of 1 ul of enzyme solution containing 5 mg/ml HcgC mixed with 1 ul of the reservoir solution : 100 mM HEPES/NaOH pH 7.5, 0.1 M NaCl, and 30% MPD (2-Methyl-2,4-pentanediol). The soaking was performed overnight in the same crystallization buffer containing 2 mM SAH and 3 mM pyridinol (dissolved in 100% DMSO).

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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: 2.05→48.55 Å / Num. obs: 65248 / % possible obs: 96.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.072 / Net I/σ(I): 6.2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9601 / CC1/2: 0.6 / Rpim(I) all: 0.498 / % possible all: 98

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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: 5O4J

5o4j


Resolution: 2.05→30.01 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9306 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 3225 4.95 %RANDOM
Rwork0.1969 ---
obs0.1988 65131 96.38 %-
Displacement parametersBiso mean: 47.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.3354 Å20 Å20.5742 Å2
2---2.2779 Å20 Å2
3---2.6133 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: 1 / Resolution: 2.05→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16777 0 212 470 17459
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1531237HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3999SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2338HARMONIC20
X-RAY DIFFRACTIONt_it17196HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.34
X-RAY DIFFRACTIONt_other_torsion14.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1174SEMIHARMONIC5
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_contact18324SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 222 4.6 %
Rwork0.2483 4600 -
all0.2495 4822 -
obs--96.38 %
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)
10.4097-0.15020.41840.68060.01281.5928-0.00950.02540.0427-0.1142-0.05320.0556-0.0592-0.10490.06270.0096-0.01060.0329-0.1995-0.00340.0961-55.946111.637925.5913
20.485-0.11460.44360.6694-0.1061.5431-0.1261-0.1447-0.00620.22360.06850.13050.0159-0.11730.05770.03930.04780.1007-0.1853-0.00130.0624-46.15993.577161.6626
30.6155-0.05260.26570.3550.08261.68820.01560.1347-0.0544-0.0887-0.0263-0.03670.08870.0650.01060.03290.03170.0803-0.1621-0.02780.0372-31.4641-12.571616.2106
40.8763-0.43280.40890.51950.42221.4039-0.1175-0.08640.2089-0.01220.1761-0.1530.11090.2896-0.0586-0.06910.05090.0414-0.1167-0.05590.0821-13.5455-3.2848.8369
5-0.0803-0.2990.12590.04810.00410.3203-0.0013-0.0054-0.0024-0.0051-0.0033-0.00650.0012-0.00140.0046-0.00030.00050.0053-0.0007-0.00310.0025-38.4414.304636.6539
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{ G|* }

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