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- PDB-6pu6: CobT from Methanocaldococcus jannaschii in complex with Alpha-Rib... -

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Basic information

Entry
Database: PDB / ID: 6pu6
TitleCobT from Methanocaldococcus jannaschii in complex with Alpha-Ribozole 5'-Phosphate, Nicotinic Acid, and Nicotinic Acid Mononucleotide
ComponentsUPF0284 protein MJ1598
KeywordsTRANSFERASE
Function / homology
Function and homology information


nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
Similarity search - Function
Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, archaeal type / Phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), large domain / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINATE MONONUCLEOTIDE / NICOTINIC ACID / ALPHA-RIBAZOLE-5'-PHOSPHATE / UPF0284 protein MJ1598
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 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 17, 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
B: UPF0284 protein MJ1598
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5135
Polymers75,6962
Non-polymers8173
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-7 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.580, 139.000, 54.490
Angle α, β, γ (deg.)90.000, 111.670, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein UPF0284 protein MJ1598


Mass: 37847.953 Da / Num. of mol.: 2
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: Chemical ChemComp-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


Mass: 335.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H14NO9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RBZ / ALPHA-RIBAZOLE-5'-PHOSPHATE


Mass: 358.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N2O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 44.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystals were formed by mixing 13.3 mg/ml protein solution containing added 1 mM 5,6-dimethylbenzimidazole and 25 mM sodium/potassium phosphate pH 7.0 with well solution containing 100 mM ...Details: Crystals were formed by mixing 13.3 mg/ml protein solution containing added 1 mM 5,6-dimethylbenzimidazole and 25 mM sodium/potassium phosphate pH 7.0 with well solution containing 100 mM MES/Acetate pH 5.5, 25% PEG 1.5K. Crystals were cryoprotected in 20% ethylene glycol, 100 mM MES/Acetate buffer pH 5.5, 16% PEG 4K, 1 mM nicotinic acid mononucleotide overnight 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: 2.293→47.5762 Å / Num. obs: 28756 / % possible obs: 97.42 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.0646 / Net I/σ(I): 15.5
Reflection shellResolution: 2.293→2.375 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.4771 / Mean I/σ(I) obs: 2.53 / Num. unique obs: 2755 / % possible all: 92.86

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0Z

3l0z


Resolution: 2.293→40.93 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.98
RfactorNum. reflection% reflection
Rfree0.2403 1433 4.99 %
Rwork0.1933 --
obs0.1956 28689 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.61 Å2 / Biso mean: 58.7454 Å2 / Biso min: 32.23 Å2
Refinement stepCycle: final / Resolution: 2.293→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 88 50 5358
Biso mean--58.85 52.59 -
Num. residues----687
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2931-2.37510.38991370.2919260793
2.3751-2.47010.32231440.2768271898
2.4701-2.58250.33721430.2623271797
2.5825-2.71870.31451420.2367268796
2.7187-2.8890.33931430.2496274398
2.889-3.11190.30621440.2366274499
3.1119-3.4250.32191440.2236272997
3.425-3.92020.21111460.1918278399
3.9202-4.93770.19421450.1547274898
4.9377-40.930.18481450.1529278098

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