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- PDB-6lcv: structure of Mutant S44P of maltooligosyltrehalose synthase from ... -

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Basic information

Entry
Database: PDB / ID: 6lcv
Titlestructure of Mutant S44P of maltooligosyltrehalose synthase from Arthrobacter ramosus
ComponentsMTSase
KeywordsISOMERASE / maltooligosyltrehalose synthase trehaolse mutant
Function / homology
Function and homology information


(1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase / (1,4)-alpha-D-glucan 1-alpha-D-glucosylmutase activity / carbohydrate metabolic process
Similarity search - Function
Maltooligosyl trehalose synthase, domain 4 / Maltooligosyl trehalose synthase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesArthrobacter ramosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsChen, C. / Su, L. / Wu, L. / Zhou, J. / Wu, J.
CitationJournal: To Be Published
Title: structure of Mutant S44P of maltooligosyltrehalose synthase from Arthrobacter ramosus
Authors: Chen, C. / Wu, J.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: 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: MTSase


Theoretical massNumber of molelcules
Total (without water)84,9151
Polymers84,9151
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26690 Å2
Unit cell
Length a, b, c (Å)194.683, 194.683, 200.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein MTSase


Mass: 84915.227 Da / Num. of mol.: 1 / Mutation: S44P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter ramosus (bacteria) / Gene: treY
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9AJN7, (1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 6.45 Å3/Da / Density % sol: 80.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Ammonium citrate tribasic and BIS-TRIS propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 53170 / % possible obs: 99.9 % / Redundancy: 25.5 % / Biso Wilson estimate: 57.31 Å2 / CC1/2: 0.992 / Net I/σ(I): 1.75
Reflection shellResolution: 2.84→2.89 Å / Num. unique obs: 2582 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZCR

5zcr


Resolution: 2.84→21.24 Å / SU ML: 0.3118 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3074
RfactorNum. reflection% reflection
Rfree0.1891 2489 5.03 %
Rwork0.1604 --
obs0.1619 49496 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.63 Å2
Refinement stepCycle: LAST / Resolution: 2.84→21.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 0 273 6153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836014
X-RAY DIFFRACTIONf_angle_d0.97148191
X-RAY DIFFRACTIONf_chiral_restr0.0502890
X-RAY DIFFRACTIONf_plane_restr0.00541098
X-RAY DIFFRACTIONf_dihedral_angle_d34.19872205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.90.33631250.3082289X-RAY DIFFRACTION83.21
2.9-2.950.31431070.27442495X-RAY DIFFRACTION89.42
2.95-3.020.32551300.2742558X-RAY DIFFRACTION93.17
3.02-3.090.33251430.25722638X-RAY DIFFRACTION95.7
3.09-3.170.31391460.23872682X-RAY DIFFRACTION97.92
3.17-3.250.25171430.22692727X-RAY DIFFRACTION98.25
3.25-3.350.24131280.20422712X-RAY DIFFRACTION98.17
3.35-3.450.25011520.18412726X-RAY DIFFRACTION98.43
3.45-3.580.20821490.17012705X-RAY DIFFRACTION98.24
3.58-3.720.20171670.16042711X-RAY DIFFRACTION98.39
3.72-3.890.1751570.14632698X-RAY DIFFRACTION97.11
3.89-4.090.13611370.12782693X-RAY DIFFRACTION96.59
4.09-4.340.15391330.11432706X-RAY DIFFRACTION96.5
4.34-4.680.13391520.10932676X-RAY DIFFRACTION95.41
4.68-5.140.12161550.11722650X-RAY DIFFRACTION94.32
5.14-5.870.16931440.13832526X-RAY DIFFRACTION89.21
5.87-7.350.1585980.1482353X-RAY DIFFRACTION80.73
7.35-21.240.15371230.13842462X-RAY DIFFRACTION81.03
Refinement TLS params.Method: refined / Origin x: -92.5555204832 Å / Origin y: 32.3868473313 Å / Origin z: 10.1996090482 Å
111213212223313233
T0.38456297273 Å20.0115979298908 Å2-0.0167376492521 Å2-0.230141702743 Å20.0175714489142 Å2--0.323800355015 Å2
L0.63594493607 °2-0.0128590085701 °2-0.0340200465089 °2-1.03332186764 °2-0.0512351074757 °2--1.10527628182 °2
S-0.040348855843 Å °-0.10211856797 Å °-0.0900048812754 Å °0.193527503287 Å °0.0552434902695 Å °-0.0415910677702 Å °0.250072448864 Å °-0.00333911356633 Å °-0.0201880409827 Å °
Refinement TLS groupSelection details: all

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