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- PDB-6pt8: Crystal Structure of CobT from Methanocaldococcus jannaschii in c... -

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Basic information

Entry
Database: PDB / ID: 6pt8
TitleCrystal Structure of CobT from Methanocaldococcus jannaschii in complex with Adenine Alpha-Ribotide and Nicotinic Acid
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
ALPHA-ADENOSINE MONOPHOSPHATE / NICOTINIC ACID / PHOSPHATE ION / UPF0284 protein MJ1598
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchwarzwalder, A.H. / Jeter, V.L. / Vecellio, A.A. / Erpenbach, E. / Escalante, 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
B: UPF0284 protein MJ1598
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8278
Polymers75,6962
Non-polymers1,1316
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-12 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.390, 138.640, 51.150
Angle α, β, γ (deg.)90.000, 108.320, 90.000
Int Tables number4
Space group name H-MP1211

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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-AAM / ALPHA-ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystals formed by mixing 1:1 ratio of 13.3 mg/mL protein solution with well solution containing 100 mM 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (HEPPS) pH 8.5 and 22% (w/v) PEG ...Details: Crystals formed by mixing 1:1 ratio of 13.3 mg/mL protein solution with well solution containing 100 mM 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (HEPPS) pH 8.5 and 22% (w/v) PEG 8K. 1 mM adenine and 50 mM Sodium/Potassium Phosphate pH 7.0 were added to protein prior to mixing with well solution. Substrates were captured in lattice prior to freezing by soaking crystals in 20% (w/v) ethylene glycol, 100 mM HEPPS pH 8.5, 22% (w/v) PEG 8K, 25 mM sodium/potassium phosophate pH 7.0, 1 mM nicotinic acid mononucleotide, and 1 mM adenine for 30 minutes. Crystals were then soaked in the same solution, but with 30% PEG 8K instead of 20% ethylene glycol and 20% PEG 8K

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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: 1.4→41.973 Å / Num. obs: 118689 / % possible obs: 98.95 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.09626 / Net I/σ(I): 12.18
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6674 / Mean I/σ(I) obs: 2.92 / Num. unique obs: 11857 / % possible all: 98.98

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0Z

3l0z


Resolution: 1.4→41.973 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.66
RfactorNum. reflection% reflection
Rfree0.1748 5933 5 %
Rwork0.1531 --
obs0.1542 118680 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.57 Å2 / Biso mean: 18.8823 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.4→41.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 106 460 5873
Biso mean--15.22 27.12 -
Num. residues----699
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.26671970.2418375199
1.4159-1.43260.26811940.2294368699
1.4326-1.450.24272020.2131382399
1.45-1.46840.23731980.2083375599
1.4684-1.48770.19611970.1956374899
1.4877-1.50810.2271990.1906378499
1.5081-1.52960.22911940.1865369499
1.5296-1.55250.21942010.1831380598
1.5525-1.57670.21491900.1757361297
1.5767-1.60260.17992000.1734380299
1.6026-1.63020.18231960.1706373199
1.6302-1.65990.18062000.1629379599
1.6599-1.69180.20571980.1617376099
1.6918-1.72630.17682000.1559379599
1.7263-1.76390.17221980.1507376199
1.7639-1.80490.18451970.1505374999
1.8049-1.850.18891980.154376998
1.85-1.90010.1721960.1449371598
1.9001-1.9560.18641980.14863769100
1.956-2.01910.17011990.1468378999
2.0191-2.09130.17871990.1466377199
2.0913-2.1750.16811990.14563779100
2.175-2.2740.16171990.1414377799
2.274-2.39380.15511960.1398372098
2.3938-2.54380.18371980.1374377199
2.5438-2.74020.17732000.14923803100
2.7402-3.01590.17041990.1578377299
3.0159-3.45210.1631930.1535367297
3.4521-4.34860.14512000.1327379899
4.3486-41.9730.15491980.1443379198

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