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- PDB-4pmu: Crystal structure of a novel reducing-end xylose-releasing exo-ol... -

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Basic information

Entry
Database: PDB / ID: 4pmu
TitleCrystal structure of a novel reducing-end xylose-releasing exo-oligoxylanase (XynA) belonging to GH10 family (space group P1211)
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process
Similarity search - Function
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.857 Å
AuthorsSantos, C.R. / Martins, V.P.M. / Zanphorlin, L.M. / Ruller, R. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/13309-0 Brazil
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Molecular mechanisms associated with xylan degradation by xanthomonas plant pathogens.
Authors: Santos, C.R. / Hoffmam, Z.B. / de Matos Martins, V.P. / Zanphorlin, L.M. / de Paula Assis, L.H. / Honorato, R.V. / Lopes de Oliveira, P.S. / Ruller, R. / Murakami, M.T.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references / Structure summary
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Feb 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
C: Endo-1,4-beta-xylanase A
D: Endo-1,4-beta-xylanase A
E: Endo-1,4-beta-xylanase A
F: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)239,0406
Polymers239,0406
Non-polymers00
Water1,63991
1
A: Endo-1,4-beta-xylanase A
B: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)79,6802
Polymers79,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-13 kcal/mol
Surface area26680 Å2
MethodPISA
2
C: Endo-1,4-beta-xylanase A
D: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)79,6802
Polymers79,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-11 kcal/mol
Surface area26440 Å2
MethodPISA
3
E: Endo-1,4-beta-xylanase A
F: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)79,6802
Polymers79,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-12 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.022, 100.741, 134.199
Angle α, β, γ (deg.)90.000, 95.150, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe enzyme is a dimer in solution as assessed by SAXS, DLS and SEC techniques.

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Components

#1: Protein
Endo-1,4-beta-xylanase A


Mass: 39839.918 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: xynA, XAC4249 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PEU1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Polyethylene glycol 6000 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.857→50 Å / Num. obs: 52305 / % possible obs: 97.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.15 / Χ2: 1.038 / Net I/av σ(I): 7.162 / Net I/σ(I): 5.8 / Num. measured all: 152136
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.857-2.922.60.6125890.9295.9
2.92-2.972.90.58625650.93898.3
2.97-3.032.90.4925971.01297.7
3.03-3.092.90.42226001.02797.3
3.09-3.1630.39125871.06897.3
3.16-3.2330.3225861.07397.3
3.23-3.3130.28225581.04796.8
3.31-3.430.25325791.05796.6
3.4-3.530.21626121.07996.8
3.5-3.6230.19225721.07796.4
3.62-3.7430.16725941.07697.3
3.74-3.892.90.15625741.05497
3.89-4.072.90.14725821.04497.1
4.07-4.292.80.13626271.06198.5
4.29-4.552.80.12326661.04299.1
4.55-4.912.80.1226621.05699.4
4.91-5.42.80.11526841.06299.6
5.4-6.182.80.1326801.04999.7
6.18-7.7830.09827031.05499.9
7.78-503.10.05826880.95196.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CNC

2cnc


Resolution: 2.857→41.15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU ML: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2651 5.1 %RANDOM
Rwork0.2107 49602 --
obs0.2133 52253 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.81 Å2 / Biso mean: 45.864 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.33 Å2
2---0.75 Å2-0 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 2.857→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16837 0 0 91 16928
Biso mean---24.71 -
Num. residues----2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01917257
X-RAY DIFFRACTIONr_angle_refined_deg0.9441.92723476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04552125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51523.401882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.284152677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.84915156
X-RAY DIFFRACTIONr_chiral_restr0.0660.22504
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02113600
X-RAY DIFFRACTIONr_mcbond_it0.6293.5158518
X-RAY DIFFRACTIONr_mcangle_it1.1055.27110637
X-RAY DIFFRACTIONr_scbond_it0.6183.5238739
LS refinement shellResolution: 2.857→2.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 169 -
Rwork0.327 3340 -
all-3509 -
obs--89.88 %
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)
11.56050.4477-0.00640.50720.10730.4539-0.0088-0.0575-0.07260.03620.0736-0.0115-0.00780.0565-0.06480.00520.01230.00690.1188-0.0010.048346.51590.388512.6776
21.2369-0.3398-0.14190.50260.14640.9075-0.06180.0133-0.05230.0653-0.0053-0.0044-0.0091-0.0250.06710.0684-0.00960.01940.02430.00970.06251.8861-4.869610.6051
31.50630.6102-0.24390.386-0.08610.2798-0.05490.2636-0.04770.02530.04120.009-0.04820.01240.01370.0435-0.05260.01070.197-0.02210.007328.4777-0.3378-30.5884
40.6029-0.1215-0.14670.464-0.0940.51390.0254-0.01750.0046-0.02290.01050.0336-0.07570.0456-0.0360.047-0.03850.02930.1304-0.01010.0412-16.57470.5101-31.9122
50.6355-0.079-0.38750.3831-0.00231.377-0.0096-0.0827-0.0269-0.0733-0.0386-0.00840.06820.02810.04820.0750.00550.02860.0929-0.04120.038310.0613-18.1336-69.3163
61.5255-0.412-0.19661.5350.0890.39250.16040.2882-0.1896-0.2362-0.16360.2336-0.14080.03720.00310.07940.0212-0.03690.1528-0.06490.0509-33.0703-9.4714-74.6422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 377
2X-RAY DIFFRACTION2B23 - 378
3X-RAY DIFFRACTION3C23 - 378
4X-RAY DIFFRACTION4D23 - 377
5X-RAY DIFFRACTION5E23 - 377
6X-RAY DIFFRACTION6F24 - 377

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