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- PDB-3lv4: Crystal structure of the glycoside hydrolase, family 43 YxiA prot... -

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Basic information

Entry
Database: PDB / ID: 3lv4
TitleCrystal structure of the glycoside hydrolase, family 43 YxiA protein from Bacillus licheniformis. Northeast Structural Genomics Consortium Target BiR14.
ComponentsGlycoside hydrolase YxiA
KeywordsHYDROLASE / Glycoside hydrolase / similar to arabinan endo-1 / 5-alpha-L-arabinosidase / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Lipocalin ...Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Glycoside hydrolase, family 43 YxiA
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.695 Å
AuthorsVorobiev, S. / Abashidze, M. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. ...Vorobiev, S. / Abashidze, M. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the glycoside hydrolase, family 43 YxiA protein from Bacillus licheniformis.
Authors: Vorobiev, S. / Abashidze, M. / Seetharaman, J. / Belote, R.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase YxiA
B: Glycoside hydrolase YxiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,05812
Polymers103,5622
Non-polymers49610
Water12,232679
1
A: Glycoside hydrolase YxiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0787
Polymers51,7811
Non-polymers2976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase YxiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9795
Polymers51,7811
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glycoside hydrolase YxiA
hetero molecules

B: Glycoside hydrolase YxiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,05812
Polymers103,5622
Non-polymers49610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_546x,y-1,z+11
Buried area3030 Å2
ΔGint-59 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.585, 60.327, 73.122
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number5
Space group name H-MC121
Detailsmonomer according to gel filtration

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Components

#1: Protein Glycoside hydrolase YxiA / YxiA / family 43 YxiA


Mass: 51781.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: DSM 13/ATCC 14580 / Gene: BL00219, BLi04220, yxiA / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) + Magic / References: UniProt: Q65D31
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 18% PEG 3350, 0.2M Ca acetate, 0.1M MES, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.695→500 Å / Num. all: 197594 / Num. obs: 192259 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.2 / Num. unique all: 19695 / % possible all: 92.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.695→45.244 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 9525 4.97 %RANDOM
Rwork0.1464 ---
obs0.1486 191496 96.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.318 Å2 / ksol: 0.405 e/Å3
Refinement stepCycle: LAST / Resolution: 1.695→45.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6929 0 25 679 7633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067136
X-RAY DIFFRACTIONf_angle_d1.0569647
X-RAY DIFFRACTIONf_dihedral_angle_d18.1442534
X-RAY DIFFRACTIONf_chiral_restr0.077974
X-RAY DIFFRACTIONf_plane_restr0.0041266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6953-1.71450.2822520.19055081X-RAY DIFFRACTION81
1.7145-1.73470.25133100.18515834X-RAY DIFFRACTION92
1.7347-1.75590.27612670.18385984X-RAY DIFFRACTION95
1.7559-1.77810.22492800.16645958X-RAY DIFFRACTION95
1.7781-1.80150.23042890.15735986X-RAY DIFFRACTION96
1.8015-1.82620.21083410.16116043X-RAY DIFFRACTION95
1.8262-1.85230.24472860.15135937X-RAY DIFFRACTION96
1.8523-1.87990.21782880.14936129X-RAY DIFFRACTION96
1.8799-1.90930.19353020.1455944X-RAY DIFFRACTION97
1.9093-1.94060.23232800.13586059X-RAY DIFFRACTION96
1.9406-1.9740.19453440.13286029X-RAY DIFFRACTION96
1.974-2.00990.19533070.12836057X-RAY DIFFRACTION96
2.0099-2.04860.17793250.11826006X-RAY DIFFRACTION97
2.0486-2.09040.19353570.11816074X-RAY DIFFRACTION97
2.0904-2.13590.16342790.12516147X-RAY DIFFRACTION97
2.1359-2.18560.1973120.13076038X-RAY DIFFRACTION98
2.1856-2.24020.18563630.12376199X-RAY DIFFRACTION98
2.2402-2.30080.17423020.11526150X-RAY DIFFRACTION99
2.3008-2.36850.16253760.12756113X-RAY DIFFRACTION99
2.3685-2.44490.19473420.13236244X-RAY DIFFRACTION99
2.4449-2.53230.19793560.12916229X-RAY DIFFRACTION99
2.5323-2.63370.19423250.13796273X-RAY DIFFRACTION100
2.6337-2.75350.21143210.14446189X-RAY DIFFRACTION100
2.7535-2.89870.17743580.14016222X-RAY DIFFRACTION99
2.8987-3.08020.1713550.14456184X-RAY DIFFRACTION99
3.0802-3.3180.17753550.14056237X-RAY DIFFRACTION99
3.318-3.65180.15673120.13666249X-RAY DIFFRACTION99
3.6518-4.17990.14583280.13736186X-RAY DIFFRACTION99
4.1799-5.26490.15473050.13716190X-RAY DIFFRACTION98
5.2649-45.25960.19733080.18416000X-RAY DIFFRACTION96

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