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

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Basic information

Entry
Database: PDB / ID: 8ork
Titlecyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus
ComponentsCyclic 2,3-diphosphoglycerate synthetase
KeywordsLIGASE / Synthetase / extremolyte / thermophilic
Function / homologycyclic 2,3-diphosphoglycerate synthase / cyclic 2,3-diphosphoglycerate synthetase activity / Cyclic 2, 3-diphospoglycerate synthetase / ligase activity / gluconeogenesis / ATP binding / cytoplasm / DI(HYDROXYETHYL)ETHER / Cyclic 2,3-diphosphoglycerate synthetase
Function and homology information
Biological speciesMethanothermus fervidus DSM 2088 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 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 14, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,34430
Polymers51,4191
Non-polymers1,92629
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.264, 105.607, 156.619
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 51418.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus DSM 2088 (archaea)
Gene: cpgS, Mfer_0077 / Plasmid: pLATE51 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O93732, cyclic 2,3-diphosphoglycerate synthase

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Non-polymers , 6 types, 323 molecules

#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 292.15 K / Method: microbatch / pH: 7.5
Details: Morpheus condition F7 consisting of 0.12 M Monosaccharides mix; 0.1M Buffer System 2 pH 7.5; 30% v/v Precipitant Mix 3 Buffer system 2: Sodium HEPES; MOPS (acid) pH7.5 Monosaccharides mix: 0. ...Details: Morpheus condition F7 consisting of 0.12 M Monosaccharides mix; 0.1M Buffer System 2 pH 7.5; 30% v/v Precipitant Mix 3 Buffer system 2: Sodium HEPES; MOPS (acid) pH7.5 Monosaccharides mix: 0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine Precipitants mix 3: 40% v/v Glycerol; 20% w/v PEG 4000
Temp details: Memmert crystals incubator

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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: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.64→42.71 Å / Num. obs: 75512 / % possible obs: 95.98 % / Redundancy: 5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.038 / Rrim(I) all: 0.086 / Net I/av σ(I): 8 / Net I/σ(I): 14.1
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 5 % / Num. unique obs: 3134 / CC1/2: 0.28 / % possible all: 60.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→42.71 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.213 --
Rwork0.177 --
obs-75512 95.98 %
Refinement stepCycle: LAST / Resolution: 1.64→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 122 294 3982

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