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- PDB-6p2n: Crystal structure of Paenibacillus graminis GH74 (PgGH74) -

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Basic information

Entry
Database: PDB / ID: 6p2n
TitleCrystal structure of Paenibacillus graminis GH74 (PgGH74)
ComponentsXyloglucanase
KeywordsHYDROLASE / glycosyl hydrolase / GH74 / xyloglucanase / 7-fold beta-propeller
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process
Similarity search - Function
Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus graminis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsStogios, P.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.
Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Attia, M.A. / Skarina, T. / Viborg, A.H. / Henrissat, B. / Savchenko, A. / Brumer, H.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xyloglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8567
Polymers80,4851
Non-polymers3716
Water22,6631258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.494, 86.214, 130.197
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 Xyloglucanase


Mass: 80484.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus graminis (bacteria) / Gene: PGRAT_12815 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A089M3R3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1258 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 5% (w/v) PEG3350, 0.2 M sodium chloride, 0.1 M sodium citrate pH 5.6, 0.5% (w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.35→35 Å / Num. obs: 136921 / % possible obs: 96.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Net I/σ(I): 31
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6842 / CC1/2: 0.567 / Rpim(I) all: 0.449 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.35→30.451 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.21
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 1954 1.51 %RANDOM
Rwork0.1494 ---
obs0.1499 132007 87.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→30.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 21 1258 6897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135924
X-RAY DIFFRACTIONf_angle_d1.2898136
X-RAY DIFFRACTIONf_dihedral_angle_d13.8882067
X-RAY DIFFRACTIONf_chiral_restr0.114874
X-RAY DIFFRACTIONf_plane_restr0.011060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36730.2084850.22865192X-RAY DIFFRACTION49
1.3673-1.38610.2526940.21936284X-RAY DIFFRACTION61
1.3861-1.40590.21551000.22557012X-RAY DIFFRACTION67
1.4059-1.42690.23951160.21737676X-RAY DIFFRACTION74
1.4269-1.44910.21581280.21648489X-RAY DIFFRACTION81
1.4491-1.47290.25581430.21299079X-RAY DIFFRACTION87
1.4729-1.49830.20941450.20429244X-RAY DIFFRACTION89
1.4983-1.52550.22551430.19719368X-RAY DIFFRACTION91
1.5255-1.55490.23221450.18729609X-RAY DIFFRACTION92
1.5549-1.58660.22241460.18569464X-RAY DIFFRACTION92
1.5866-1.62110.221540.17969552X-RAY DIFFRACTION91
1.6211-1.65880.19181420.17369423X-RAY DIFFRACTION91
1.6588-1.70030.20041430.1679462X-RAY DIFFRACTION91
1.7003-1.74630.21031430.15889349X-RAY DIFFRACTION90
1.7463-1.79770.19961460.15759251X-RAY DIFFRACTION89
1.7977-1.85570.18561410.15599309X-RAY DIFFRACTION89
1.8557-1.9220.19091400.1519317X-RAY DIFFRACTION89
1.922-1.99890.15591390.13949449X-RAY DIFFRACTION91
1.9989-2.08990.15841470.13779527X-RAY DIFFRACTION92
2.0899-2.20.16261490.13849830X-RAY DIFFRACTION94
2.2-2.33780.15191570.142410020X-RAY DIFFRACTION96
2.3378-2.51830.19651620.145910292X-RAY DIFFRACTION99
2.5183-2.77150.20171550.146610379X-RAY DIFFRACTION100
2.7715-3.17220.14951610.138810390X-RAY DIFFRACTION100
3.1722-3.99520.16921580.117910393X-RAY DIFFRACTION100
3.9952-30.4590.16311540.142610201X-RAY DIFFRACTION98
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)
10.4641-0.1562-0.3330.530.43351.0674-0.0249-0.0386-0.02550.04430.0258-0.11680.08560.11580.00260.10170.0046-0.00340.10330.00530.131145.66543.04748.7526
21.50990.4444-0.56311.1293-0.44611.5424-0.0219-0.1346-0.15370.01780.0096-0.04360.16410.1052-0.02690.09530.0003-0.01490.0783-0.00050.109244.120850.15768.4477
30.52290.06880.0720.5460.54961.3384-0.00670.0335-0.06750.0437-0.06350.06450.0918-0.07960.06930.10560.00360.00920.112-0.00290.132322.141341.891760.4614
45.02394.23323.01285.93836.01116.8971-0.25220.16340.21510.10760.02810.31190.0328-0.01810.22450.09990.0157-0.01580.15440.04970.156224.716753.221148.3134
50.6234-0.9201-0.35281.82960.7570.51120.01950.0864-0.0444-0.041-0.04410.0748-0.0369-0.09690.03120.0707-0.0059-0.00250.1229-0.01470.092830.180731.122440.8753
61.915-0.53750.19651.0386-0.08490.80560.0069-0.0886-0.16390.0912-0.01710.14070.0765-0.12280.01210.106-0.0210.00390.0805-0.00720.114839.99775.531641.6548
71.6306-0.16880.5322.53470.00311.50110.0381-0.1301-0.00480.18-0.0194-0.22250.06010.0078-0.01350.06680.00140.01030.07760.00240.114358.879417.576936.6126
81.71190.1518-0.90681.60990.57271.91570.0439-0.07550.108-0.002-0.0189-0.0914-0.12-0.0043-0.01570.07770.01120.00340.05730.00510.091450.270329.517933.6165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 34:160)
2X-RAY DIFFRACTION2(chain A and resid 161:263)
3X-RAY DIFFRACTION3(chain A and resid 264:417)
4X-RAY DIFFRACTION4(chain A and resid 418:423)
5X-RAY DIFFRACTION5(chain A and resid 424:506)
6X-RAY DIFFRACTION6(chain A and resid 507:638)
7X-RAY DIFFRACTION7(chain A and resid 639:735)
8X-RAY DIFFRACTION8(chain A and resid 736:781)

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