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- PDB-6ptf: Crystal Structure of CobT from Methanocaldococcus jannaschii in A... -

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Basic information

Entry
Database: PDB / ID: 6ptf
TitleCrystal Structure of CobT from Methanocaldococcus jannaschii in Apo State
ComponentsUPF0284 protein MJ1598
KeywordsTRANSFERASE
Function / homologyNicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, archaeal type / Phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / UPF0284 protein MJ1598
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsSchwarzwalder, A.H. / Jeter, V.L. / Vecellio, A.A. / Erpenbach, E. / Escalante-Semerena, J.C. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM130399 United States
CitationJournal: Sci Rep / Year: 2022
Title: Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria.
Authors: Jeter, V.L. / Schwarzwalder, A.H. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0284 protein MJ1598


Theoretical massNumber of molelcules
Total (without water)37,8481
Polymers37,8481
Non-polymers00
Water63135
1
A: UPF0284 protein MJ1598

A: UPF0284 protein MJ1598


Theoretical massNumber of molelcules
Total (without water)75,6962
Polymers75,6962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1860 Å2
ΔGint-10 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.010, 56.010, 243.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

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Components

#1: Protein UPF0284 protein MJ1598 / CobT


Mass: 37847.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1598 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58993
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystals formed by mixing 13.3 mg/ml protein solution with well solution containing 8.4% PEG 8K, 100 mM MES/ acetate buffer pH 5.5, 1 mM 5-hydroxybenzimidazole. Crystals were cryoprotected ...Details: Crystals formed by mixing 13.3 mg/ml protein solution with well solution containing 8.4% PEG 8K, 100 mM MES/ acetate buffer pH 5.5, 1 mM 5-hydroxybenzimidazole. Crystals were cryoprotected by overnight soak in 20% ethylene glycol, 100 mM MES/acetate buffer pH 5.5, 16% Peg 4K and 5 mM 5,6-dimethylbenzimidazole prior to freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.203→46.1 Å / Num. obs: 20650 / % possible obs: 99.68 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05481 / Net I/σ(I): 24.59
Reflection shellResolution: 2.203→2.282 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.6916 / Mean I/σ(I) obs: 3.15 / Num. unique obs: 1997 / CC1/2: 0.969 / % possible all: 99.35

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0z

3l0z


Resolution: 2.203→46.097 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.34
RfactorNum. reflection% reflection
Rfree0.2447 1030 5 %
Rwork0.2046 --
obs0.2066 20599 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.86 Å2 / Biso mean: 67.0932 Å2 / Biso min: 34.67 Å2
Refinement stepCycle: final / Resolution: 2.203→46.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 0 35 2618
Biso mean---60.36 -
Num. residues----339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2032-2.31930.32541430.2723271199
2.3193-2.46460.33421430.2474271599
2.4646-2.65490.29591450.25822745100
2.6549-2.92210.26241450.24442740100
2.9221-3.34480.28171460.24092788100
3.3448-4.21360.25311490.20482831100
4.2136-46.0970.20231590.16893039100

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