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- PDB-3dr5: Crystal structure of the Q8NRD3_CORGL protein from Corynebacteriu... -

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Basic information

Entry
Database: PDB / ID: 3dr5
TitleCrystal structure of the Q8NRD3_CORGL protein from Corynebacterium glutamicum. Northeast Structural Genomics Consortium target CgR117.
ComponentsPutative O-Methyltransferase
Keywordsstructural genomics / unknown function / Q8NRD3 / Cgl1119 / PF01596 / O-METHYLTRANSFERASE / CgR117 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Methyltransferase / Transferase
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q8NRD3_CORGL protein from Corynebacterium glutamicum.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Foote, E.L. / Mao, L. / Xiao, R. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative O-Methyltransferase


Theoretical massNumber of molelcules
Total (without water)24,0051
Polymers24,0051
Non-polymers00
Water3,063170
1
A: Putative O-Methyltransferase

A: Putative O-Methyltransferase


Theoretical massNumber of molelcules
Total (without water)48,0112
Polymers48,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area4090 Å2
ΔGint-23 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.511, 50.511, 303.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

DetailsAuthors state that the biological unit is Dimer according to aggregation screening. The second symmetry mate is generated by x,x-y+1,-z+7/6.

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Components

#1: Protein Putative O-Methyltransferase / PROBABLE O-METHYLTRANSFERASE


Mass: 24005.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032/DSM 20300/JCM 1318/ LMG 3730/NCIMB 10025 / Gene: Cgl1119, cg1270 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q8NRD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 10% PEG 4000, 0.1M magnesium chloride, 0.1M MES, pH6.15, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 19601 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 22.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.6 / Num. unique all: 8205 / % possible all: 69.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→43.3 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 281023.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 942 5.4 %RANDOM
Rwork0.211 ---
obs0.211 17601 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.8008 Å2 / ksol: 0.335338 e/Å3
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.26 Å24.43 Å20 Å2
2--7.26 Å20 Å2
3----14.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.25→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 0 170 1781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 100 4.7 %
Rwork0.241 2025 -
obs--61.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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