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- PDB-5z6p: The crystal structure of an agarase, AgWH50C -

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Basic information

Entry
Database: PDB / ID: 5z6p
TitleThe crystal structure of an agarase, AgWH50C
ComponentsB-agarase
KeywordsHYDROLASE / Glucoside hydrolase 50 family / agarase activity
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Agarase, CBM-like domain / Agarase CBM like domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Galactose-binding lectin / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel ...Agarase, CBM-like domain / Agarase CBM like domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Galactose-binding lectin / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesAgarivorans gilvus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.061 Å
AuthorsMao, X. / Zhou, J. / Zhang, P. / Zhang, L. / Zhang, J. / Li, Y.
CitationJournal: Appl. Microbiol. Biotechnol. / Year: 2019
Title: Structure-based design of agarase AgWH50C from Agarivorans gilvus WH0801 to enhance thermostability.
Authors: Zhang, P. / Zhang, J. / Zhang, L. / Sun, J. / Li, Y. / Wu, L. / Zhou, J. / Xue, C. / Mao, X.
History
DepositionJan 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 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: B-agarase
B: B-agarase


Theoretical massNumber of molelcules
Total (without water)173,6482
Polymers173,6482
Non-polymers00
Water17,565975
1
A: B-agarase


Theoretical massNumber of molelcules
Total (without water)86,8241
Polymers86,8241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: B-agarase


Theoretical massNumber of molelcules
Total (without water)86,8241
Polymers86,8241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)215.801, 93.647, 85.049
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein B-agarase


Mass: 86824.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agarivorans gilvus (bacteria) / Strain: WH0801 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A023LLI1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED RESIDUE 307 GLY IN DATABASE A0A023LLI1 WAS WRONG. RESIDUE 307 SHOULD BE ASP.

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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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5
Details: 0.2M Na iodide, 0.1M Bis Tris propane, pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 98307 / % possible obs: 98.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 23.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.594 / Num. unique obs: 4283 / Rsym value: 0.594 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.10.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BQ2

4bq2


Resolution: 2.061→46.824 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2448 4570 4.93 %
Rwork0.1951 --
obs0.1976 92718 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.061→46.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10802 0 0 975 11777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811109
X-RAY DIFFRACTIONf_angle_d1.11615055
X-RAY DIFFRACTIONf_dihedral_angle_d14.4423969
X-RAY DIFFRACTIONf_chiral_restr0.0491540
X-RAY DIFFRACTIONf_plane_restr0.0051972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0611-2.08450.3401890.23161614X-RAY DIFFRACTION51
2.0845-2.1090.2933930.21662235X-RAY DIFFRACTION70
2.109-2.13470.34511070.21392312X-RAY DIFFRACTION73
2.1347-2.16170.26971460.21122363X-RAY DIFFRACTION76
2.1617-2.19020.24711520.2092472X-RAY DIFFRACTION78
2.1902-2.22020.26441360.21952631X-RAY DIFFRACTION82
2.2202-2.25190.26631340.22252652X-RAY DIFFRACTION85
2.2519-2.28550.29981430.22842787X-RAY DIFFRACTION87
2.2855-2.32120.2831400.22052874X-RAY DIFFRACTION90
2.3212-2.35930.30851490.2252984X-RAY DIFFRACTION93
2.3593-2.40.28571600.21823020X-RAY DIFFRACTION95
2.4-2.44360.26171660.22383066X-RAY DIFFRACTION97
2.4436-2.49060.29551740.2313092X-RAY DIFFRACTION98
2.4906-2.54140.28081690.22743109X-RAY DIFFRACTION99
2.5414-2.59670.311690.21343170X-RAY DIFFRACTION100
2.5967-2.65710.3341750.22673165X-RAY DIFFRACTION100
2.6571-2.72350.28431560.21033172X-RAY DIFFRACTION100
2.7235-2.79720.25231700.20623163X-RAY DIFFRACTION100
2.7972-2.87950.26421770.21423204X-RAY DIFFRACTION100
2.8795-2.97240.27181530.20753150X-RAY DIFFRACTION100
2.9724-3.07860.24331580.20573209X-RAY DIFFRACTION100
3.0786-3.20180.24961840.19853132X-RAY DIFFRACTION99
3.2018-3.34750.25221660.19143176X-RAY DIFFRACTION99
3.3475-3.5240.21351520.18363191X-RAY DIFFRACTION100
3.524-3.74470.20151510.183207X-RAY DIFFRACTION100
3.7447-4.03360.19681540.1663209X-RAY DIFFRACTION100
4.0336-4.43930.19841630.1543182X-RAY DIFFRACTION100
4.4393-5.0810.20471840.15543164X-RAY DIFFRACTION99
5.081-6.39890.20621400.19513225X-RAY DIFFRACTION99
6.3989-46.83560.24161600.19943218X-RAY DIFFRACTION97

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