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- PDB-3ms8: Enzyme-Substrate interactions of IXT6, the intracellular xylanase... -

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Basic information

Entry
Database: PDB / ID: 3ms8
TitleEnzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.
ComponentsIntra-cellular xylanase ixt6
KeywordsHYDROLASE / Xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
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 / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Its 2Q8X only one point mutation, using its phases doing rigid, annealing / Resolution: 1.7 Å
AuthorsSolomon, V. / Zolotnitsky, G. / Alhadeff, R. / Shoham, Y. / Shoham, G.
CitationJournal: TO BE PUBLISHED
Title: Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.
Authors: Solomon, V. / Zolotnitsky, G. / Alhadeff, R. / Shoham, Y. / Shoham, G.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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.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_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

Downloads & links

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Assembly

Deposited unit
A: Intra-cellular xylanase ixt6
B: Intra-cellular xylanase ixt6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,87210
Polymers77,2742
Non-polymers5998
Water7,981443
1
A: Intra-cellular xylanase ixt6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9365
Polymers38,6371
Non-polymers2994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intra-cellular xylanase ixt6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9365
Polymers38,6371
Non-polymers2994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.389, 80.081, 79.026
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Intra-cellular xylanase ixt6


Mass: 38636.832 Da / Num. of mol.: 2 / Mutation: E241A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: T-6 / Gene: xynA2 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09LY9, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH=6.5, 1.9M soduim acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.7→19.89 Å / Num. all: 319380 / Num. obs: 110960 / % possible obs: 97 % / Observed criterion σ(I): 15.3 / Redundancy: 2.88 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.76 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 5019 / Rsym value: 0.161 / % possible all: 88.5

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Its 2Q8X only one point mutation, using its phases doing rigid, annealing
Starting model: PDB ENTRY 2Q8X

2q8x


Resolution: 1.7→19.89 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5384 -RANDOM
Rwork0.196 ---
all-107077 --
obs-107077 92.9 %-
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--13.02 Å20 Å2-2.02 Å2
2--17.81 Å20 Å2
3----4.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5385 0 38 443 5866
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBOND LENGTHS0.005
X-RAY DIFFRACTIONBOND ANGLES1.3
X-RAY DIFFRACTIONIMPROPER ANGLES0.8
X-RAY DIFFRACTIONDIHEDRAL ANGLES22.1
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.332 753 -
Rwork0.3 --
obs-13750 75.4 %

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