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- PDB-8fa4: Crystal structure of Xanthomonas campestris GanA beta-galactosidase -

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Basic information

Entry
Database: PDB / ID: 8fa4
TitleCrystal structure of Xanthomonas campestris GanA beta-galactosidase
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / beta-galactosidase / xanthomonas
Function / homologyDomain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / beta-galactosidase complex / beta-galactosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glycoside hydrolase
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsGodoy, A.S. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011/05712-3 Brazil
CitationJournal: To Be Published
Title: Crystal structure of Xanthomonas campestris GanA beta-galactosidase
Authors: Godoy, A.S. / Polikarpov, I.
History
DepositionNov 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycoside hydrolase
A: Glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)121,8452
Polymers121,8452
Non-polymers00
Water29,2921626
1
B: Glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)60,9221
Polymers60,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)60,9221
Polymers60,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.132, 158.132, 94.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Glycoside hydrolase


Mass: 60922.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: XC_2481 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2X862
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1626 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M trilithium citrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.699→48.16 Å / Num. obs: 131695 / % possible obs: 100 % / Redundancy: 16.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.047 / Rrim(I) all: 0.191 / Net I/σ(I): 14.1
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.3 % / Redundancy: 16 % / Rmerge(I) obs: 1.506 / Num. measured all: 102559 / Num. unique obs: 6396 / CC1/2: 0.733 / Rpim(I) all: 0.384 / Rrim(I) all: 1.555 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHENIXv1refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→46.074 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 2000 1.52 %
Rwork0.1609 --
obs0.1614 131641 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→46.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8045 0 0 1626 9671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118344
X-RAY DIFFRACTIONf_angle_d1.32611400
X-RAY DIFFRACTIONf_dihedral_angle_d13.3923021
X-RAY DIFFRACTIONf_chiral_restr0.0651176
X-RAY DIFFRACTIONf_plane_restr0.0081521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6995-1.7420.27911400.23099101X-RAY DIFFRACTION99
1.742-1.78910.23721410.20929159X-RAY DIFFRACTION100
1.7891-1.84170.23341420.19589149X-RAY DIFFRACTION100
1.8417-1.90120.23561420.18739192X-RAY DIFFRACTION100
1.9012-1.96910.2281400.17919140X-RAY DIFFRACTION100
1.9691-2.0480.21971420.16999192X-RAY DIFFRACTION100
2.048-2.14120.21011430.16119209X-RAY DIFFRACTION100
2.1412-2.2540.19591420.16149213X-RAY DIFFRACTION100
2.254-2.39530.20551420.16429244X-RAY DIFFRACTION100
2.3953-2.58020.19411430.16439234X-RAY DIFFRACTION100
2.5802-2.83980.20721430.16289289X-RAY DIFFRACTION100
2.8398-3.25060.20061430.1599325X-RAY DIFFRACTION100
3.2506-4.09510.16831460.13549414X-RAY DIFFRACTION100

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