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- PDB-4e4p: Second native structure of Xylanase A1 from Paenibacillus sp. JDR-2 -

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Basic information

Entry
Database: PDB / ID: 4e4p
TitleSecond native structure of Xylanase A1 from Paenibacillus sp. JDR-2
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / xylanase / Paenibacillus / TIM barrel / beta/alpha 8 fold
Function / homology
Function and homology information


cell wall / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 ...Carbohydrate family 9 binding domain-like / Carbohydrate-binding domain, family 9 / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsPozharski, E. / St John, F.J.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2.
Authors: St John, F.J. / Preston, J.F. / Pozharski, E.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Endo-1,4-beta-xylanase A
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9728
Polymers76,8042
Non-polymers1686
Water4,053225
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4864
Polymers38,4021
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4864
Polymers38,4021
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.518, 58.528, 65.024
Angle α, β, γ (deg.)90.000, 108.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endo-1,4-beta-xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 38401.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PCR cloned GH10 catalytic domain from a 8-module xylanase having a N-terminal His tag with a thrombin cleavage site for removal
Source: (gene. exp.) Paenibacillus sp. (bacteria) / Strain: JDR-2 / Gene: Pjdr2_0221, xynA, xynA1 / Plasmid: pETXynA1CD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6CRV0, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 294.5 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM MgCl2, 100mM HEPES sodium salt, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.5K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→84.82 Å / Num. obs: 48561 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.109 / Χ2: 1.055 / Net I/σ(I): 3.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.92-2748451.0581100
2-2.087.247931.0711100
2.08-2.177.448631.03311000.805
2.17-2.297.448081.14111000.661
2.29-2.437.548621.07411000.485
2.43-2.627.548361.07411000.345
2.62-2.887.548461.11911000.222
2.88-3.37.448571.06311000.131
3.3-4.167.448980.97411000.07
4.16-507.249530.946198.90.05

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 12.726 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 2440 5 %RANDOM
Rwork0.2534 ---
obs0.2555 48381 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.98 Å2 / Biso mean: 44.588 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å21.24 Å2
2---1.81 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 6 225 4875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224748
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9316452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32825.702242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40815788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0581514
X-RAY DIFFRACTIONr_chiral_restr0.1410.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213658
X-RAY DIFFRACTIONr_mcbond_it1.131.52914
X-RAY DIFFRACTIONr_mcangle_it1.91124678
X-RAY DIFFRACTIONr_scbond_it3.52531834
X-RAY DIFFRACTIONr_scangle_it5.3784.51774
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.543 153 -
Rwork0.48 3062 -
all-3215 -
obs--88.64 %
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)
19.85853.12191.34725.3483-1.73324.59220.186-0.0127-1.2806-0.2308-0.4552-1.08960.92561.29590.26920.48480.21870.02640.54230.15720.289723.78-36.48924.206
21.0660.3690.3491.9043-1.12813.59530.07810.0468-0.1592-0.0975-0.0986-0.00840.31870.04520.02040.2564-0.0151-0.00410.1699-0.0020.02942.239-26.92417.732
32.30181.2122-1.15482.9833-2.46494.85370.1420.18320.22890.1160.00470.0414-0.6125-0.0931-0.14670.2210.00750.00160.15880.00040.06793.315-12.55115.151
43.09522.024-3.26394.8394-4.19088.16630.0431-0.0709-0.02330.2478-0.23620.0023-0.12260.36970.19320.2016-0.0517-0.0760.18240.02020.015912.019-15.45422.573
54.9572-2.3476-2.55523.891.55934.52550.0470.01170.17450.0565-0.2648-0.2291-0.27250.59980.21780.2594-0.0699-0.06360.36410.10370.062419.973-15.15420.012
64.8061-0.2561-1.41283.530.831813.0138-0.19670.08350.0098-0.1822-0.1402-0.46860.0411.85670.33690.18150.0616-0.01450.69210.22170.18430.534-23.23618.896
79.65473.26691.891610.6198-1.65554.85370.0813-0.0655-1.3953-0.0347-0.4746-1.24621.08111.39590.39330.48810.23680.08840.59550.19260.270814.341-7.32155.588
82.0418-0.12480.71651.8939-1.18284.00210.11960.0258-0.0901-0.127-0.1138-0.0380.37530.0341-0.00580.2604-0.026-0.00140.1516-0.00690.0237-8.3811.60548.712
93.51352.8193-1.87972.4445-3.99125.26290.11940.26020.29870.27640.00320.2925-0.6155-0.0184-0.12260.2520.0122-0.01180.1579-0.00550.068-6.36817.60144.279
103.32832.0813-3.6125.4892-4.52348.39680.0664-0.08740.02420.2527-0.2129-0.0197-0.11190.3940.14650.1882-0.0528-0.07130.18320.01520.01811.46513.35453.542
117.2636-9.9202-5.12315.75698.438710.3103-0.1248-0.37240.50170.783-0.0298-0.3222-0.24160.00110.15460.3445-0.11450.0040.2246-0.03180.0527-1.16219.45559.308
124.2913-1.1327-1.79845.39160.4326.8634-0.03330.06570.101-0.1329-0.1985-0.367-0.03981.19880.23180.1766-0.0192-0.05720.58120.16410.091317.1198.9947.928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 46
2X-RAY DIFFRACTION2A47 - 146
3X-RAY DIFFRACTION3A147 - 176
4X-RAY DIFFRACTION4A177 - 213
5X-RAY DIFFRACTION5A214 - 268
6X-RAY DIFFRACTION6A277 - 305
7X-RAY DIFFRACTION7B5 - 42
8X-RAY DIFFRACTION8B43 - 143
9X-RAY DIFFRACTION9B144 - 175
10X-RAY DIFFRACTION10B176 - 211
11X-RAY DIFFRACTION11B212 - 231
12X-RAY DIFFRACTION12B232 - 305

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