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- PDB-1nq6: Crystal Structure of the catalytic domain of xylanase A from Stre... -

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Basic information

Entry
Database: PDB / ID: 1nq6
TitleCrystal Structure of the catalytic domain of xylanase A from Streptomyces halstedii JM8
ComponentsXys1
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 10 / XYLANASE / XYLAN DEGRADATION
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsCanals, A. / Vega, M.C. / Gomis-Ruth, F.X. / Santamaria, R.I. / Coll, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of xylanase Xys1delta from Streptomyces halstedii.
Authors: Canals, A. / Vega, M.C. / Gomis-Ruth, F.X. / Diaz, M. / Santamaria R, R.I. / Coll, M.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: Xys1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6382
Polymers32,6141
Non-polymers241
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.050, 79.600, 87.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xys1


Mass: 32614.070 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Strain: JM8 / Gene: xysA / Plasmid: pJM9 / Production host: Streptomyces parvulus (bacteria) / Strain (production host): JI2283 / References: UniProt: Q59922, endo-1,4-beta-xylanase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 1.61 Å3/Da / Density % sol: 22.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, MAGNESIUM CHLORIDE, SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
210 %PEG40001reservoir
30.1 M1reservoirMgCl2
40.1 Msodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.885 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1996
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.782→24.818 Å / Num. all: 23589 / Num. obs: 22905 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.453 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.1
Reflection shellResolution: 1.78→1.88 Å / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 8.9 / % possible all: 85.8
Reflection
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 25 Å / Redundancy: 3.4 % / Num. measured all: 78251
Reflection shell
*PLUS
% possible obs: 85.8 % / Redundancy: 2.7 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E0W

1e0w


Resolution: 1.78→24.82 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.269 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17643 1658 7.3 %RANDOM
Rwork0.14515 ---
all0.1484 22865 --
obs0.14745 21207 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.78→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 1 341 2639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212357
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9173200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295301
X-RAY DIFFRACTIONr_chiral_restr0.0820.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021843
X-RAY DIFFRACTIONr_nbd_refined0.1910.2916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.235
X-RAY DIFFRACTIONr_mcbond_it0.3871.51493
X-RAY DIFFRACTIONr_mcangle_it0.71722374
X-RAY DIFFRACTIONr_scbond_it1.2453862
X-RAY DIFFRACTIONr_scangle_it1.954.5821
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.218 90
Rwork0.163 1118
obs-1118
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8023-0.3863-0.85511.0435-0.1080.88020.13390.0587-0.0112-0.1049-0.10620.02910.0413-0.0292-0.02770.04740.01740.00170.0488-0.01010.02396.2512-12.19734.0898
20.00750.3190.10530.15480.14440.4761-0.00740.0326-0.0505-0.04060.00670.0020.0287-0.01040.00080.03490.00960.00420.037-0.00390.03815.4149-2.287613.8189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2A1002 - 1035
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.09
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.16

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