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- PDB-4w84: Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1... -

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Basic information

Entry
Database: PDB / ID: 4w84
TitleCrystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in the native form
ComponentsXyloglucan-specific endo-beta-1,4-glucanase
KeywordsHYDROLASE / glycoside hydrolase cell wall degrading enzyme GH5 family
Function / homology
Function and homology information


xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Xyloglucan-specific endo-beta-1,4-glucanase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.79 Å
AuthorsSantos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/13309-0; 2014/07135-1 Brazil
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis for Xyloglucan Specificity and alpha-d-Xylp(1 6)-d-Glcp Recognition at the -1 Subsite within the GH5 Family.
Authors: Dos Santos, C.R. / Cordeiro, R.L. / Wong, D.W. / Murakami, M.T.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
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 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 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_struct_conn_angle / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xyloglucan-specific endo-beta-1,4-glucanase
B: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1416
Polymers76,8482
Non-polymers2934
Water8,413467
1
A: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5703
Polymers38,4241
Non-polymers1462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xyloglucan-specific endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5703
Polymers38,4241
Non-polymers1462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.241, 97.241, 95.678
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Xyloglucan-specific endo-beta-1,4-glucanase


Mass: 38423.809 Da / Num. of mol.: 2 / Fragment: unp residues 92-430
Source method: isolated from a genetically manipulated source
Details: cow's rumen
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
References: UniProt: D2K7Z0, xyloglucan-specific endo-beta-1,4-glucanase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, PEG400, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.979, 0.932
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9321
ReflectionResolution: 1.79→50 Å / Num. obs: 190946 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 26.04 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.114 / Χ2: 1.178 / Net I/σ(I): 11.95 / Num. measured all: 1056374
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obsMean I/σ(I) obs
1.79-1.890.5215735831202300321.67896.3
1.89-2.020.80516895929198291850.91000.8182.31
2.02-2.190.90815708327052270460.4861000.4424.29
2.19-2.390.96714582425096250860.2921000.2657.1
2.39-2.680.98512509822620226070.18799.90.16910.45
2.68-3.090.99510575019904198950.1051000.09516.58
3.09-3.780.9988520016916168850.05899.80.05227
3.78-5.330.9996929112998129910.03999.90.03540.62
5.330.99941811724272190.03299.70.02946.51

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.7.3_928)refinement
PDB_EXTRACT3.15data extraction
SHELXDEphasing
XSCALEdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.79→31.607 Å / FOM work R set: 0.8629 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 4805 5.02 %random
Rwork0.1783 181323 --
obs0.1796 190903 99.32 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.307 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 78.79 Å2 / Biso mean: 28.49 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.7248 Å2-0 Å2-0 Å2
2--1.7248 Å2-0 Å2
3----3.4495 Å2
Refinement stepCycle: final / Resolution: 1.79→31.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5385 0 42 467 5894
Biso mean--42.29 34.32 -
Num. residues----679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075553
X-RAY DIFFRACTIONf_angle_d0.9787581
X-RAY DIFFRACTIONf_chiral_restr0.067813
X-RAY DIFFRACTIONf_plane_restr0.004983
X-RAY DIFFRACTIONf_dihedral_angle_d12.3141969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7857-1.8060.38682620.3392520884
1.806-1.82720.33533270.321588699
1.8272-1.84950.34692860.31036165100
1.8495-1.87290.30763490.30566139100
1.8729-1.89760.33483120.28326043100
1.8976-1.92350.31833140.26595977100
1.9235-1.9510.28613130.25826118100
1.951-1.98010.25033060.2416178100
1.9801-2.01110.25963020.21666031100
2.0111-2.0440.2573440.21516046100
2.044-2.07933606107100
2.0793-2.11710.22192900.20416054100
2.1171-2.15780.23613200.20086085100
2.1578-2.20180.21383580.18646036100
2.2018-2.24970.2123560.18016069100
2.2497-2.3020.23373080.19516112100
2.302-2.35960.20652830.18556179100
2.3596-2.42330.23113240.18376039100
2.4233-2.49460.21723020.17926075100
2.4946-2.57510.21483240.17396103100
2.5751-2.66710.21653640.17396012100
2.6671-2.77380.18312720.17336171100
2.7738-2.90.20123380.17686032100
2.9-3.05280.21753260.17166035100
3.0528-3.24380.18143280.17246108100
3.2438-3.4940.19732850.1676054100
3.494-3.84510.16863210.15046093100
3.8451-4.40020.14733620.13276079100
4.4002-5.53890.15673160.14116016100
5.53890.1833280.16416073100

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