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- PDB-3lb9: Crystal structure of the B. circulans cpA123 circular permutant -

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Basic information

Entry
Database: PDB / ID: 3lb9
TitleCrystal structure of the B. circulans cpA123 circular permutant
ComponentsEndo-1,4-beta-xylanaseXylanase
KeywordsHYDROLASE / permutation / BcX / Glycosidase / Xylan degradation
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsD'Angelo, I. / Reitinger, S. / Ludwiczek, M. / Strynadka, N. / Withers, S.G. / Mcintosh, L.P.
CitationJournal: Biochemistry / Year: 2010
Title: Circular permutation of Bacillus circulans xylanase: a kinetic and structural study.
Authors: Reitinger, S. / Yu, Y. / Wicki, J. / Ludwiczek, M. / D'Angelo, I. / Baturin, S. / Okon, M. / Strynadka, N.C. / Lutz, S. / Withers, S.G. / McIntosh, L.P.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: struct_keywords / struct_ref_seq_dif
Item: _struct_keywords.text / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_pdb_strand_id
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
C: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)59,9753
Polymers59,9753
Non-polymers00
Water72140
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)19,9921
Polymers19,9921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)19,9921
Polymers19,9921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-1,4-beta-xylanase

C: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)39,9832
Polymers39,9832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2840 Å2
ΔGint-9 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.810, 114.970, 65.030
Angle α, β, γ (deg.)90.00, 113.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endo-1,4-beta-xylanase / Xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase


Mass: 19991.615 Da / Num. of mol.: 3 / Fragment: residues 65-182 and 2-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: xlnA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21( DE3) / References: UniProt: P09850, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 298 K / pH: 8
Details: 13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2008 / Details: OSMICS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 10649 / % possible obs: 92 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.147 / Rsym value: 0.148 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 1147 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.412 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HV1

1hv1


Resolution: 3→19.88 Å / SU ML: 0.49 / σ(F): 1.49 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 473 5.01 %
Rwork0.192 --
obs0.195 9443 100 %
all-9834 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2.52 Å2 / ksol: 0.34 e/Å3
Refinement stepCycle: LAST / Resolution: 3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 0 40 4294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034409
X-RAY DIFFRACTIONf_angle_d0.6886050
X-RAY DIFFRACTIONf_dihedral_angle_d17.6011390
X-RAY DIFFRACTIONf_chiral_restr0.049616
X-RAY DIFFRACTIONf_plane_restr0.006767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.43240.33261570.23472979X-RAY DIFFRACTION100
3.4324-4.31710.28851570.1792980X-RAY DIFFRACTION100
4.3171-19.87670.19931590.16933011X-RAY DIFFRACTION100

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