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- PDB-5jvv: Crystal structure and characterization an elongating GH family 16... -

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Basic information

Entry
Database: PDB / ID: 5jvv
TitleCrystal structure and characterization an elongating GH family 16 beta-1,3-glucosyltransferase
Componentsbeta-1,3-glucosyltransferase
KeywordsTRANSFERASE / glucoside hydrolase / beta-1 / 3-glucosyltransferase
Function / homology
Function and homology information


endo-1,3(4)-beta-glucanase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / side of membrane / plasma membrane
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
endo-1,3(4)-beta-glucanase
Similarity search - Component
Biological speciesPaecilomyces sp. J18 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å
AuthorsQin, Z. / Yan, Q. / Yang, S. / Jiang, Z.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Catalytic Mechanism of a Novel Glycoside Hydrolase Family 16 "Elongating" beta-Transglycosylase
Authors: Qin, Z. / Yang, S. / Zhao, L. / You, X. / Yan, Q. / Jiang, Z.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 8, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: beta-1,3-glucosyltransferase
A: beta-1,3-glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)65,0822
Polymers65,0822
Non-polymers00
Water12,592699
1
B: beta-1,3-glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)32,5411
Polymers32,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: beta-1,3-glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)32,5411
Polymers32,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.282, 91.469, 59.532
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein beta-1,3-glucosyltransferase


Mass: 32540.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paecilomyces sp. J18 (fungus) / Strain: J18
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: A0A1S4NYE9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: 35% PEG 3350, 0.1M Na-Citrate pH4.4 / PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.589→37.17 Å / Num. obs: 62905 / % possible obs: 96.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.93
Reflection shellResolution: 1.589→1.65 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 6.11 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDT

3wdt


Resolution: 1.589→37.167 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.04
RfactorNum. reflection% reflection
Rfree0.1789 1991 3.17 %
Rwork0.1487 --
obs0.1496 62895 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.589→37.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 0 699 5257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064730
X-RAY DIFFRACTIONf_angle_d1.1216434
X-RAY DIFFRACTIONf_dihedral_angle_d12.4061678
X-RAY DIFFRACTIONf_chiral_restr0.08701
X-RAY DIFFRACTIONf_plane_restr0.005841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5888-1.62850.22291340.15264200X-RAY DIFFRACTION93
1.6285-1.67250.22661400.15334359X-RAY DIFFRACTION97
1.6725-1.72170.19231440.15494322X-RAY DIFFRACTION97
1.7217-1.77730.18731490.15474324X-RAY DIFFRACTION97
1.7773-1.84080.16661280.1554289X-RAY DIFFRACTION95
1.8408-1.91450.18911510.14864365X-RAY DIFFRACTION98
1.9145-2.00170.22141390.1474391X-RAY DIFFRACTION98
2.0017-2.10720.20221530.15064362X-RAY DIFFRACTION97
2.1072-2.23920.16761390.14914310X-RAY DIFFRACTION95
2.2392-2.41210.16881440.14814411X-RAY DIFFRACTION98
2.4121-2.65470.18081480.15344417X-RAY DIFFRACTION98
2.6547-3.03870.22881410.15974356X-RAY DIFFRACTION97
3.0387-3.82790.14971450.144435X-RAY DIFFRACTION98
3.8279-37.17710.15391360.14294363X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 3.6466 Å / Origin y: -23.8877 Å / Origin z: -14.6415 Å
111213212223313233
T0.0794 Å20.0035 Å20.0102 Å2-0.086 Å20.0081 Å2--0.0831 Å2
L0.1808 °20.0537 °20.0607 °2-0.2635 °20.133 °2--0.164 °2
S0.0157 Å °0.0102 Å °-0.0155 Å °-0.0147 Å °-0.0023 Å °-0.0306 Å °0.0005 Å °-0.0047 Å °-0.0118 Å °
Refinement TLS groupSelection details: all

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