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- PDB-7kv0: Crystallographic structure of Paenibacillus xylanivorans GH11 -

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Basic information

Entry
Database: PDB / ID: 7kv0
TitleCrystallographic structure of Paenibacillus xylanivorans GH11
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Glycoside Hydrolase / GH11
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / 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, 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
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesPaenibacillus sp. A59 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsBriganti, L. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel88882.328729/2019-01 Brazil
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase.
Authors: Briganti, L. / Capetti, C. / Pellegrini, V.O.A. / Ghio, S. / Campos, E. / Nascimento, A.S. / Polikarpov, I.
History
DepositionNov 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8645
Polymers40,6782
Non-polymers1863
Water1,892105
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4633
Polymers20,3391
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4012
Polymers20,3391
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.426, 62.995, 183.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Endo-1,4-beta-xylanase


Mass: 20338.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. A59 (bacteria) / Gene: AMS66_16445 / Plasmid: pJExpress / Details (production host): NdeI/XbaI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M9BNX9, endo-1,4-beta-xylanase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium citrate tribasic dihydrate 1.6 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4585 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4585 Å / Relative weight: 1
ReflectionResolution: 2.5→45.8 Å / Num. obs: 12915 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.5-2.612.61.814520.545199.7
9.02-45.811.40.0753210.996199.8

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z79

2z79


Resolution: 2.501→45.8 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 651 5.06 %
Rwork0.2142 12216 -
obs0.2158 12867 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.67 Å2 / Biso mean: 45.6536 Å2 / Biso min: 37.52 Å2
Refinement stepCycle: final / Resolution: 2.501→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 12 105 2999
Biso mean--47.95 45 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022989
X-RAY DIFFRACTIONf_angle_d0.5444085
X-RAY DIFFRACTIONf_dihedral_angle_d8.7571610
X-RAY DIFFRACTIONf_chiral_restr0.042418
X-RAY DIFFRACTIONf_plane_restr0.002523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5013-2.69440.31541340.29882393
2.6944-2.96550.311150.27472420
2.9655-3.39450.28921520.23972399
3.3945-4.27620.22311110.20332451
4.2762-45.80.20841390.17322553

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