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- PDB-3czl: Crystal Structure Analysis of Sucrose hydrolase(SUH) E322Q-glucos... -

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Basic information

Entry
Database: PDB / ID: 3czl
TitleCrystal Structure Analysis of Sucrose hydrolase(SUH) E322Q-glucose complex
Componentssucrose hydrolase
KeywordsHYDROLASE / (alpha/beta)8-barrel
Function / homology
Function and homology information


amylosucrase activity / carbohydrate metabolic process / hydrolase activity
Similarity search - Function
: / Sucrose hydrolase-like, C-terminal domain / Amylosucrase, catalytic domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Rna Polymerase Sigma Factor; Chain: A / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain ...: / Sucrose hydrolase-like, C-terminal domain / Amylosucrase, catalytic domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Rna Polymerase Sigma Factor; Chain: A / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Amylosucrase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. glycines (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, M.I. / Rhee, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures and mutagenesis of sucrose hydrolase from Xanthomonas axonopodis pv. glycines: insight into the exclusively hydrolytic amylosucrase fold.
Authors: Kim, M.I. / Kim, H.S. / Jung, J. / Rhee, S.
History
DepositionApr 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sucrose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6002
Polymers70,4201
Non-polymers1801
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.800, 119.100, 55.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein sucrose hydrolase


Mass: 70420.070 Da / Num. of mol.: 1 / Mutation: E322Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. glycines (bacteria)
Strain: 8ra / Gene: supH / Plasmid: pET41b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q6UVM5, sucrose alpha-glucosidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.28 Å3/Da / Density % sol: 45.95 % / Mosaicity: 0.334 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M HEPES, 0.2M calcium acetate, 16% PEG 3000, 5mM DTT, 0.1M cesium chloride , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44083 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.054 / Χ2: 1.17 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.143 / Num. unique all: 4001 / Χ2: 0.581 / % possible all: 91.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CZE

3cze


Resolution: 2→50 Å
RfactorNum. reflection% reflection
Rfree0.248 4205 9.5 %
Rwork0.203 --
obs-41583 94 %
Solvent computationBsol: 51.731 Å2
Displacement parametersBiso mean: 28.778 Å2
Baniso -1Baniso -2Baniso -3
1--1.596 Å20 Å20 Å2
2--6.265 Å20 Å2
3----4.668 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 12 398 5162
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5031.5
X-RAY DIFFRACTIONc_scbond_it2.4952
X-RAY DIFFRACTIONc_mcangle_it2.1192
X-RAY DIFFRACTIONc_scangle_it3.0752.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3dna-rna_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5glc.param

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