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- PDB-8oru: cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophil... -

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Basic information

Entry
Database: PDB / ID: 8oru
Titlecyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus bound to 2,3-diphosphoglycerate and ADP.
ComponentsCyclic 2,3-diphosphoglycerate synthetase
KeywordsLIGASE / Synthetase / extremolyte / thermophilic
Function / homology
Function and homology information


cyclic 2,3-diphosphoglycerate synthase / cyclic 2,3-diphosphoglycerate synthetase activity / ligase activity / gluconeogenesis / ATP binding / cytoplasm
Similarity search - Function
Cyclic 2, 3-diphospoglycerate synthetase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / (2R)-2,3-diphosphoglyceric acid / PHOSPHATE ION / Cyclic 2,3-diphosphoglycerate synthetase
Similarity search - Component
Biological speciesMethanothermus fervidus DSM 2088 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsDe Rose, S.A. / Isupov, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Front Microbiol / Year: 2023
Title: Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus .
Authors: De Rose, S.A. / Isupov, M.N. / Worthy, H.L. / Stracke, C. / Harmer, N.J. / Siebers, B. / Littlechild, J.A.
History
DepositionApr 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Cyclic 2,3-diphosphoglycerate synthetase
BBB: Cyclic 2,3-diphosphoglycerate synthetase
CCC: Cyclic 2,3-diphosphoglycerate synthetase
DDD: Cyclic 2,3-diphosphoglycerate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,17634
Polymers202,8994
Non-polymers4,27730
Water90150
1
AAA: Cyclic 2,3-diphosphoglycerate synthetase
BBB: Cyclic 2,3-diphosphoglycerate synthetase
hetero molecules


  • defined by software
  • Evidence: gel filtration
  • 104 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)103,66718
Polymers101,4492
Non-polymers2,21716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-70 kcal/mol
Surface area36020 Å2
MethodPISA
2
CCC: Cyclic 2,3-diphosphoglycerate synthetase
DDD: Cyclic 2,3-diphosphoglycerate synthetase
hetero molecules


  • defined by software
  • 104 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)103,50916
Polymers101,4492
Non-polymers2,06014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-60 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.234, 71.478, 103.543
Angle α, β, γ (deg.)97.015, 103.424, 99.045
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Cyclic 2,3-diphosphoglycerate synthetase / cDPGS


Mass: 50724.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus DSM 2088 (archaea)
Gene: cpgS, Mfer_0077 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: O93732, cyclic 2,3-diphosphoglycerate synthase

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Non-polymers , 6 types, 80 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DG2 / (2R)-2,3-diphosphoglyceric acid / 2,3-Bisphosphoglyceric acid / 2,3-bisphosphoglycerate / 2,3-BPG / 2,3-diphosphoglyceric acid / 2,3-diphosphoglycerate / 2,3-DPG / (2~{R})-2,3-diphosphonooxypropanoic acid / 2,3-Bisphosphoglyceric acid


Mass: 266.037 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O10P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


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

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Details

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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 292.15 K / Method: microbatch / pH: 8.5
Details: The substrate bound crystals grew in condition E12 of the Morpheus screen consisting of 0.12M Ethylene glycols mix, 0.1M Buffer System 3 pH 8.5 and 37.5% v/v of Precipitant Mix 4. where the ...Details: The substrate bound crystals grew in condition E12 of the Morpheus screen consisting of 0.12M Ethylene glycols mix, 0.1M Buffer System 3 pH 8.5 and 37.5% v/v of Precipitant Mix 4. where the different solution are: Ethylene glycols mix: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol. Buffer system 3: Tris (base); BICINE pH 8.5 Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.23→69.92 Å / Num. obs: 92153 / % possible obs: 97.7 % / Redundancy: 1.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.115 / Net I/σ(I): 6.3
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 1.9 % / Num. unique obs: 4558 / CC1/2: 0.382 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→69.92 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.256 --
Rwork0.216 --
obs-92153 85.28 %
Refinement stepCycle: LAST / Resolution: 2.23→69.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14232 0 255 50 14537

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