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- PDB-1n82: The high-resolution crystal structure of IXT6, a thermophilic, in... -

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Basic information

Entry
Database: PDB / ID: 1n82
TitleThe high-resolution crystal structure of IXT6, a thermophilic, intracellular xylanase from G. stearothermophilus
Componentsintra-cellular xylanase
KeywordsHYDROLASE
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 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSolomon, V. / Teplitsky, A. / Golan, G. / Gilboa, R. / Reiland, V. / Shulami, S. / Moryles, S. / Zolotnitsky, G. / Shoham, Y. / Shoham, G.
CitationJournal: To be Published
Title: The high-resolution crystal structure of IXT6, a thermophilic, intracellular xylanase from G. stearothermophilus
Authors: Solomon, V. / Teplitsky, A. / Golan, G. / Gilboa, R. / Reiland, V. / Shulami, S. / Moryles, S. / Zolotnitsky, G. / Shoham, Y. / Shoham, G.
History
DepositionNov 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: intra-cellular xylanase
B: intra-cellular xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,72718
Polymers77,3922
Non-polymers1,33516
Water9,566531
1
A: intra-cellular xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,54811
Polymers38,6961
Non-polymers85210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: intra-cellular xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1797
Polymers38,6961
Non-polymers4836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.481, 80.579, 79.054
Angle α, β, γ (deg.)90.00, 91.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein intra-cellular xylanase / Xylanase


Mass: 38695.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T-6 / Gene: XYNA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q9ZFM8, UniProt: Q09LY9*PLUS, endo-1,4-beta-xylanase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 3.07 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH=6.5, 1.9M sodium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.11
ReflectionResolution: 1.45→38 Å / Num. obs: 171850 / % possible obs: 91.6 % / Observed criterion σ(I): 18.1 / Redundancy: 7 % / Biso Wilson estimate: 22.252 Å2 / Rsym value: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4882 / Rsym value: 0.342 / % possible all: 52.3

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: initial model of Xylanase T-6 (family 10) of Bacillus stearothermophilus.

Resolution: 1.45→15 Å / Num. parameters: 54899 / Num. restraintsaints: 68938 / Cross valid method: FREE R / σ(F): 0 / Details: CNS 1.0 was also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 6719 4.3 %RANDOM
Rwork0.1589 ---
all-171850 --
obs-171850 91.6 %-
Displacement parametersBiso mean: 22.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å / Num. disordered residues: 26 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5987.55
Refinement stepCycle: LAST / Resolution: 1.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 86 531 5997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.093

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