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- PDB-3vzj: Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylan... -

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Basic information

Entry
Database: PDB / ID: 3vzj
TitleCrystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / xylanase / GH-11 glycoside hydrolase
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: 2.406 Å
AuthorsLudwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P.
CitationJournal: Biochemistry / Year: 2013
Title: Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase
Authors: Ludwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Brockerman, J.A. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P.
History
DepositionOct 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8646
Polymers81,6724
Non-polymers1922
Water1,33374
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5142
Polymers20,4181
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,4181
Polymers20,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,4181
Polymers20,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5142
Polymers20,4181
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.174, 86.737, 73.090
Angle α, β, γ (deg.)90.00, 89.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20418.037 Da / Num. of mol.: 4 / Mutation: E172H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: xlnA / Production host: Escherichia coli (E. coli) / References: UniProt: P09850, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.4→38.167 Å / Num. all: 35327 / Num. obs: 31471 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34 Å2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HV1

1hv1


Resolution: 2.406→38.167 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6371 / SU ML: 0.59 / σ(F): 1.41 / Phase error: 40.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3434 832 5.1 %RANDOM
Rwork0.2388 ---
all0.24 17143 --
obs0.2442 16311 64.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.951 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 30.8582 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.1806 Å20 Å2-0.0108 Å2
2---0.761 Å2-0 Å2
3---1.9416 Å2
Refinement stepCycle: LAST / Resolution: 2.406→38.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 10 74 5880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086000
X-RAY DIFFRACTIONf_angle_d1.2378232
X-RAY DIFFRACTIONf_chiral_restr0.085836
X-RAY DIFFRACTIONf_plane_restr0.0061048
X-RAY DIFFRACTIONf_dihedral_angle_d20.6841900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4064-2.55710.41241190.33532367248660
2.5571-2.75450.47841480.33292735288368
2.7545-3.03160.36531450.30122694283968
3.0316-3.470.38381400.23692649278966
3.47-4.37090.31031390.1962560269964
4.3709-38.17220.26051410.16822474261561

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