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- PDB-8faa: Crystal structure of Xanthomonas campestris GH35 beta-galactosidase -

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Basic information

Entry
Database: PDB / ID: 8faa
TitleCrystal structure of Xanthomonas campestris GH35 beta-galactosidase
ComponentsBeta-galactosidase
KeywordsHYDROLASE / beta-galactosidase / xanthomonas
Function / homology
Function and homology information


vacuole / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
G: Beta-galactosidase
H: Beta-galactosidase
I: Beta-galactosidase
J: Beta-galactosidase
K: Beta-galactosidase
L: Beta-galactosidase
M: Beta-galactosidase
N: Beta-galactosidase
O: Beta-galactosidase
P: Beta-galactosidase


Theoretical massNumber of molelcules
Total (without water)887,66416
Polymers887,66416
Non-polymers00
Water52,1712896
1
E: Beta-galactosidase
G: Beta-galactosidase

A: Beta-galactosidase

C: Beta-galactosidase
K: Beta-galactosidase

I: Beta-galactosidase
M: Beta-galactosidase
P: Beta-galactosidase


Theoretical massNumber of molelcules
Total (without water)443,8328
Polymers443,8328
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_555-x,y+1/2,-z1
2
B: Beta-galactosidase
D: Beta-galactosidase
F: Beta-galactosidase
H: Beta-galactosidase
J: Beta-galactosidase
N: Beta-galactosidase
O: Beta-galactosidase

L: Beta-galactosidase


Theoretical massNumber of molelcules
Total (without water)443,8328
Polymers443,8328
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)128.271, 162.991, 235.478
Angle α, β, γ (deg.)90.00, 92.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-galactosidase


Mass: 55478.988 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: XCC2404 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P844
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2896 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: calcium acetate 0.2M PEG3350 20%

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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: 2.5→49.1 Å / Num. obs: 332061 / % possible obs: 99.1 % / Redundancy: 4.2 % / CC1/2: 0.98 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 15162 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHENIXv1refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.1 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 16767 5.05 %
Rwork0.2111 --
obs0.2131 332061 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62736 0 0 2896 65632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664528
X-RAY DIFFRACTIONf_angle_d0.84688160
X-RAY DIFFRACTIONf_dihedral_angle_d6.3178992
X-RAY DIFFRACTIONf_chiral_restr0.0529264
X-RAY DIFFRACTIONf_plane_restr0.00911904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.520.37595190.32449262X-RAY DIFFRACTION88
2.52-2.550.36846000.316410547X-RAY DIFFRACTION100
2.55-2.580.3285950.285610499X-RAY DIFFRACTION100
2.58-2.620.31856040.279610516X-RAY DIFFRACTION100
2.62-2.650.32585780.281810523X-RAY DIFFRACTION100
2.65-2.690.32375260.283510359X-RAY DIFFRACTION98
2.69-2.730.31175280.273710612X-RAY DIFFRACTION100
2.73-2.770.33615420.272310620X-RAY DIFFRACTION100
2.77-2.810.32125650.274810523X-RAY DIFFRACTION100
2.81-2.860.32645950.278210496X-RAY DIFFRACTION100
2.86-2.910.31325810.268910538X-RAY DIFFRACTION100
2.91-2.960.31195180.26810598X-RAY DIFFRACTION100
2.96-3.020.31945810.264610590X-RAY DIFFRACTION100
3.02-3.080.28125940.248410539X-RAY DIFFRACTION100
3.08-3.140.29355570.246110591X-RAY DIFFRACTION100
3.14-3.220.29135370.23610618X-RAY DIFFRACTION100
3.22-3.30.27295680.232610432X-RAY DIFFRACTION99
3.3-3.390.27285760.233310534X-RAY DIFFRACTION100
3.39-3.490.2545510.225210354X-RAY DIFFRACTION98
3.49-3.60.2395690.211110558X-RAY DIFFRACTION100
3.6-3.730.23795230.205610396X-RAY DIFFRACTION98
3.73-3.880.24315970.194310559X-RAY DIFFRACTION100
3.88-4.050.22685330.183310363X-RAY DIFFRACTION98
4.05-4.270.18965470.159610598X-RAY DIFFRACTION100
4.27-4.530.18385210.155610647X-RAY DIFFRACTION100
4.53-4.880.19215520.148510602X-RAY DIFFRACTION100
4.88-5.370.1755320.153210688X-RAY DIFFRACTION100
5.37-6.150.20065590.16410668X-RAY DIFFRACTION100
6.15-7.740.20415550.172910714X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 47.3601 Å / Origin y: -76.6771 Å / Origin z: 59.1644 Å
111213212223313233
T0.1058 Å2-0.0012 Å20.0163 Å2-0.1017 Å2-0.0194 Å2--0.1208 Å2
L-0.0041 °20.0013 °20.0529 °2--0.0291 °2-0.0026 °2--0.0343 °2
S-0.0243 Å °-0.0168 Å °0.005 Å °0.0162 Å °-0.0104 Å °-0.004 Å °-0.0114 Å °0 Å °-0.055 Å °
Refinement TLS groupSelection details: all

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