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- PDB-2mzb: Solution structural studies of GTP:adenosylcobinamide-phosphate g... -

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Basic information

Entry
Database: PDB / ID: 2mzb
TitleSolution structural studies of GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) from Methanocaldococcus jannaschii
ComponentsAdenosylcobinamide-phosphate guanylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / nucleotidyltransferase activity / GTP binding
Similarity search - Function
Conserved hypothetical protein CHP00454 / MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Adenosylcobinamide-phosphate guanylyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing
Model detailslowest energy, model1
AuthorsSingarapu, K. / Otte, M. / Tonelli, M. / Westler, W.M. / Escalante-Semerena, J.C. / Markley, J.L.
CitationJournal: Plos One / Year: 2015
Title: Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii.
Authors: Singarapu, K.K. / Otte, M.M. / Tonelli, M. / Westler, W.M. / Escalante-Semerena, J.C. / Markley, J.L.
History
DepositionFeb 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosylcobinamide-phosphate guanylyltransferase


Theoretical massNumber of molelcules
Total (without water)21,7701
Polymers21,7701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Adenosylcobinamide-phosphate guanylyltransferase / / AdoCbi-P guanylyltransferase


Mass: 21770.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: cobY, MJ1117 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58517, adenosylcobinamide-phosphate guanylyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution NMR Structure of CobY
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D CBCA(CO)NH
1523D HNCO
1623D H(CCO)NH
1723D (H)CCH-TOCSY
1823D 1H-15N NOESY
1923D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM [U-100% 15N] CobY, 2.0 mM [U-100% 15N] CobY, 2.0 mM [U-100% 15N] CobY, 2.0 mM [U-100% 15N] CobY, 2.0 mM [U-100% 15N] CobY, 2.0 mM [U-100% 15N] CobY, 90% H2O/10% D2O90% H2O/10% D2O
22.0 mM [U-100% 13C; U-100% 15N] CobY, 2.0 mM [U-100% 13C; U-100% 15N] CobY, 2.0 mM [U-100% 13C; U-100% 15N] CobY, 2.0 mM [U-100% 13C; U-100% 15N] CobY, 2.0 mM [U-100% 13C; U-100% 15N] CobY, 2.0 mM [U-100% 13C; U-100% 15N] CobY, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMCobY-1[U-100% 15N]1
2.0 mMCobY-2[U-100% 15N]1
2.0 mMCobY-3[U-100% 15N]1
2.0 mMCobY-4[U-100% 15N]1
2.0 mMCobY-5[U-100% 15N]1
2.0 mMCobY-6[U-100% 15N]1
2.0 mMCobY-7[U-100% 13C; U-100% 15N]2
2.0 mMCobY-8[U-100% 13C; U-100% 15N]2
2.0 mMCobY-9[U-100% 13C; U-100% 15N]2
2.0 mMCobY-10[U-100% 13C; U-100% 15N]2
2.0 mMCobY-11[U-100% 13C; U-100% 15N]2
2.0 mMCobY-12[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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