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- PDB-4hu8: Crystal Structure of a Bacterial Ig-like Domain Containing GH10 X... -

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Basic information

Entry
Database: PDB / ID: 4hu8
TitleCrystal Structure of a Bacterial Ig-like Domain Containing GH10 Xylanase from Termite Gut
ComponentsGH10 Xylanase
KeywordsHYDROLASE / (alpha/beta)8 barrel / Big2 / glycoside hydrolase / bacterial Ig-like domain
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Immunoglobulin-like - #1080 / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2 / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 ...Immunoglobulin-like - #1080 / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2 / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGlobitermes brachycerastes (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHan, Q. / Liu, N. / Robinson, H. / Cao, L. / Qian, C. / Wang, Q. / Xie, L. / Ding, H. / Wang, Q. / Huang, Y. ...Han, Q. / Liu, N. / Robinson, H. / Cao, L. / Qian, C. / Wang, Q. / Xie, L. / Ding, H. / Wang, Q. / Huang, Y. / Li, J. / Zhou, Z.
CitationJournal: Biotechnol.Bioeng. / Year: 2013
Title: Biochemical characterization and crystal structure of a GH10 xylanase from termite gut bacteria reveal a novel structural feature and significance of its bacterial Ig-like domain.
Authors: Han, Q. / Liu, N. / Robinson, H. / Cao, L. / Qian, C. / Wang, Q. / Xie, L. / Ding, H. / Wang, Q. / Huang, Y. / Li, J. / Zhou, Z.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: GH10 Xylanase
B: GH10 Xylanase
C: GH10 Xylanase
D: GH10 Xylanase
E: GH10 Xylanase
F: GH10 Xylanase
G: GH10 Xylanase
H: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,82731
Polymers409,6628
Non-polymers2,16623
Water38,6962148
1
A: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3963
Polymers51,2081
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4924
Polymers51,2081
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5805
Polymers51,2081
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4924
Polymers51,2081
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3963
Polymers51,2081
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4003
Polymers51,2081
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4884
Polymers51,2081
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: GH10 Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5845
Polymers51,2081
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.685, 86.963, 246.433
Angle α, β, γ (deg.)92.96, 90.86, 108.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GH10 Xylanase


Mass: 51207.707 Da / Num. of mol.: 8 / Fragment: GH10 Xylanase catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Globitermes brachycerastes (cockroach) / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: K7PDC1*PLUS, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Fragment: Big_2 domain / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2148 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate, 2 M ammonium sulfate, 20% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 293766 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nq6

1nq6


Resolution: 2→49.08 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26624 14505 5.1 %RANDOM
Rwork0.21876 ---
obs0.22115 272472 96.86 %-
all-293766 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.467 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28562 0 126 2148 30836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229321
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.94239709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48553606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.124.3861368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.174155004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.78715160
X-RAY DIFFRACTIONr_chiral_restr0.0910.24293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122264
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 943 -
Rwork0.278 17590 -
obs--84.66 %

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