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- PDB-6jak: OtsA apo structure -

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Basic information

Entry
Database: PDB / ID: 6jak
TitleOtsA apo structure
ComponentsTrehalose-6-phosphate synthase
KeywordsTRANSFERASE / Trehalose-6-phosphate synthase
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / response to osmotic stress / response to stress / DNA damage response
Similarity search - Function
Alpha,alpha-trehalose-phosphate synthase / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trehalose-6-phosphate synthase / Trehalose-6-phosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsWang, S. / Zhao, Y. / Wang, D. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFD0300700 China
CitationJournal: Biochem.J. / Year: 2019
Title: Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1.
Authors: Wang, S. / Zhao, Y. / Yi, L. / Shen, M. / Wang, C. / Zhang, X. / Yang, J. / Peng, Y.L. / Wang, D. / Liu, J.
History
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase
C: Trehalose-6-phosphate synthase
D: Trehalose-6-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)206,1064
Polymers206,1064
Non-polymers00
Water4,360242
1
A: Trehalose-6-phosphate synthase
B: Trehalose-6-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)103,0532
Polymers103,0532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-10 kcal/mol
Surface area35860 Å2
MethodPISA
2
C: Trehalose-6-phosphate synthase
D: Trehalose-6-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)103,0532
Polymers103,0532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-10 kcal/mol
Surface area36060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 119.660, 99.430
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Trehalose-6-phosphate synthase / OtsA / Osmoregulatory trehalose synthesis protein A / UDP-glucose-glucosephosphate glucosyltransferase


Mass: 51526.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: otsA, NCTC9077_02568 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A376VH75, UniProt: P31677*PLUS, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.41→87.42 Å / Num. obs: 75262 / % possible obs: 95.3 % / Redundancy: 7.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.41→2.47 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7695 / CC1/2: 0.685 / Rpim(I) all: 0.521

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UQU

1uqu


Resolution: 2.41→29.687 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2314 3733 4.96 %
Rwork0.1803 --
obs0.1828 75245 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.41→29.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14355 0 0 242 14597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414716
X-RAY DIFFRACTIONf_angle_d1.49320005
X-RAY DIFFRACTIONf_dihedral_angle_d16.428767
X-RAY DIFFRACTIONf_chiral_restr0.0862182
X-RAY DIFFRACTIONf_plane_restr0.0112598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.44050.32021280.25382719X-RAY DIFFRACTION98
2.4405-2.47260.35041220.252715X-RAY DIFFRACTION97
2.4726-2.50650.32211460.25032690X-RAY DIFFRACTION97
2.5065-2.54220.27711460.23132690X-RAY DIFFRACTION98
2.5422-2.58020.27931340.2262695X-RAY DIFFRACTION97
2.5802-2.62050.2951620.21842657X-RAY DIFFRACTION97
2.6205-2.66340.28041200.21252695X-RAY DIFFRACTION97
2.6634-2.70930.29331240.2022667X-RAY DIFFRACTION97
2.7093-2.75850.27471280.21222716X-RAY DIFFRACTION96
2.7585-2.81150.29691480.21482611X-RAY DIFFRACTION95
2.8115-2.86890.30781430.21222601X-RAY DIFFRACTION94
2.8689-2.93120.25651460.20542606X-RAY DIFFRACTION93
2.9312-2.99930.28711430.21692484X-RAY DIFFRACTION90
2.9993-3.07430.29861120.21182229X-RAY DIFFRACTION81
3.0743-3.15730.29761640.21642531X-RAY DIFFRACTION92
3.1573-3.25010.27531480.20172686X-RAY DIFFRACTION97
3.2501-3.35490.23961490.19542736X-RAY DIFFRACTION99
3.3549-3.47460.22811510.18332716X-RAY DIFFRACTION98
3.4746-3.61350.25351400.18092754X-RAY DIFFRACTION98
3.6135-3.77760.22511240.1672721X-RAY DIFFRACTION98
3.7776-3.97640.21791260.16542748X-RAY DIFFRACTION97
3.9764-4.22480.18451500.1592679X-RAY DIFFRACTION97
4.2248-4.550.19111260.1492698X-RAY DIFFRACTION96
4.55-5.00590.20831140.14472675X-RAY DIFFRACTION95
5.0059-5.72580.22041500.17722461X-RAY DIFFRACTION89
5.7258-7.19680.21371340.19432538X-RAY DIFFRACTION90
7.1968-29.68920.17261550.14742794X-RAY DIFFRACTION98

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