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- PDB-6lcu: structure of maltooligosyltrehalose synthase from Arthrobacter ramosus -

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Basic information

Entry
Database: PDB / ID: 6lcu
Titlestructure of maltooligosyltrehalose synthase from Arthrobacter ramosus
ComponentsMTSase
KeywordsISOMERASE / maltooligosyltrehalose synthase trehalose
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 / alpha-glucan catabolic process / trehalose biosynthetic process
Similarity search - Function
Maltooligosyl trehalose synthase, domain 4 / Maltooligosyl trehalose synthase; domain 4 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Arc Repressor Mutant, subunit A / Glycoside hydrolase superfamily ...Maltooligosyl trehalose synthase, domain 4 / Maltooligosyl trehalose synthase; domain 4 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase, domain 2 / Maltooligosyl trehalose synthase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Arc Repressor Mutant, subunit A / Glycoside hydrolase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesArthrobacter ramosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChen, C. / Su, L. / Wu, L. / Zhou, J. / Wu, J.
CitationJournal: To Be Published
Title: structure 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

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Assembly

Deposited unit
A: MTSase


Theoretical massNumber of molelcules
Total (without water)84,9051
Polymers84,9051
Non-polymers00
Water10,359575
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 area26610 Å2
Unit cell
Length a, b, c (Å)195.430, 195.430, 197.727
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
Components on special symmetry positions
IDModelComponents
11A-821-

HOH

21A-934-

HOH

31A-1029-

HOH

41A-1181-

HOH

51A-1224-

HOH

61A-1361-

HOH

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Components

#1: Protein MTSase


Mass: 84905.188 Da / Num. of mol.: 1
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.: 575 / 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: 6.42 Å3/Da / Density % sol: 80.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 81790 / % possible obs: 100 % / Redundancy: 21 % / Biso Wilson estimate: 39.22 Å2 / CC1/2: 0.997 / Net I/σ(I): 1.85
Reflection shellResolution: 2.45→2.49 Å / Num. unique obs: 4011 / CC1/2: 0.718

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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: 2.45→50 Å / SU ML: 0.2378 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5798
RfactorNum. reflection% reflection
Rfree0.1776 4112 5.06 %
Rwork0.1537 --
obs0.1549 81790 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.98 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5880 0 0 575 6455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00976013
X-RAY DIFFRACTIONf_angle_d1.0398189
X-RAY DIFFRACTIONf_chiral_restr0.1796890
X-RAY DIFFRACTIONf_plane_restr0.00571098
X-RAY DIFFRACTIONf_dihedral_angle_d35.03982204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.31281320.26952497X-RAY DIFFRACTION94.88
2.48-2.510.26111150.24452585X-RAY DIFFRACTION97.12
2.51-2.540.24561280.24342572X-RAY DIFFRACTION97.72
2.54-2.570.29141490.23822590X-RAY DIFFRACTION97.86
2.57-2.610.2841330.23612600X-RAY DIFFRACTION98.91
2.61-2.650.25171550.23112620X-RAY DIFFRACTION99.5
2.65-2.690.25261420.22532619X-RAY DIFFRACTION99.93
2.69-2.730.24441530.2272626X-RAY DIFFRACTION100
2.73-2.770.29231460.22072639X-RAY DIFFRACTION99.96
2.77-2.820.22221270.20612653X-RAY DIFFRACTION100
2.82-2.870.281450.21072646X-RAY DIFFRACTION100
2.87-2.930.23911450.20042649X-RAY DIFFRACTION100
2.93-2.990.24811400.19612647X-RAY DIFFRACTION100
2.99-3.050.2571460.1882651X-RAY DIFFRACTION100
3.05-3.120.22581440.18312641X-RAY DIFFRACTION100
3.12-3.20.19991390.17532670X-RAY DIFFRACTION100
3.2-3.290.18511460.16082643X-RAY DIFFRACTION100
3.29-3.380.18141560.14682664X-RAY DIFFRACTION100
3.38-3.490.14151430.12542663X-RAY DIFFRACTION100
3.49-3.620.12391270.12052692X-RAY DIFFRACTION100
3.62-3.760.11751380.11282685X-RAY DIFFRACTION100
3.76-3.930.12881450.10712675X-RAY DIFFRACTION100
3.93-4.140.12931700.1062661X-RAY DIFFRACTION100
4.14-4.40.10831420.1032698X-RAY DIFFRACTION100
4.4-4.740.11351330.09922722X-RAY DIFFRACTION100
4.74-5.220.13511260.11512749X-RAY DIFFRACTION100
5.22-5.970.17291430.14062744X-RAY DIFFRACTION100
5.97-7.520.17631600.15542784X-RAY DIFFRACTION100
7.52-48.860.16431440.16342914X-RAY DIFFRACTION98.61
Refinement TLS params.Method: refined / Origin x: -93.2257933485 Å / Origin y: 32.5157817655 Å / Origin z: 10.2670959761 Å
111213212223313233
T0.302045307619 Å2-0.00136141889588 Å20.0133750513676 Å2-0.196707379456 Å20.00469199570333 Å2--0.276359245048 Å2
L0.620860511143 °20.169960530802 °2-0.0207659973287 °2-0.861861467092 °2-0.0808937092648 °2--1.21686628188 °2
S0.0210937695485 Å °-0.108220079628 Å °-0.0901752505097 Å °0.110853137309 Å °-0.0157280760311 Å °-0.000729949263184 Å °0.242726667491 Å °0.0124670447098 Å °-0.0120746510829 Å °
Refinement TLS groupSelection details: all

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