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- PDB-5u2o: Crystal structure of Zn-binding triple mutant of GH family 9 endo... -

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Basic information

Entry
Database: PDB / ID: 5u2o
TitleCrystal structure of Zn-binding triple mutant of GH family 9 endoglucanase J30
ComponentsJ30 CCH
KeywordsHYDROLASE / glycoside hydrolase / GH9 / Ig-like domain / CBM30
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set ...Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Immunoglobulin E-set / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / J30 cch
Similarity search - Component
Biological speciesThermobacillus composti KWC4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsEllinghaus, T.L. / Pereira, J.H. / McAndrew, R.P. / Welner, D.H. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Engineering glycoside hydrolase stability by the introduction of zinc binding.
Authors: Ellinghaus, T.L. / Pereira, J.H. / McAndrew, R.P. / Welner, D.H. / DeGiovanni, A.M. / Guenther, J.M. / Tran, H.M. / Feldman, T. / Simmons, B.A. / Sale, K.L. / Adams, P.D.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO ...SHEET DETERMINATION METHOD: AUTHOR THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2 AND 3 OF SHEETS AA2 AND AA3 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: J30 CCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6107
Polymers63,9871
Non-polymers6236
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.960, 90.960, 316.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein J30 CCH


Mass: 63987.066 Da / Num. of mol.: 1 / Mutation: A98C, G114C, Y143H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobacillus composti KWC4 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E0U3*PLUS
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: trisodium citrate dihydrate, 2-propanol, PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.46→70.51 Å / Num. obs: 134366 / % possible obs: 99.8 % / Redundancy: 21.5 % / Biso Wilson estimate: 13.36 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 17.8
Reflection shellResolution: 1.46→1.5 Å / Redundancy: 21.7 % / Rmerge(I) obs: 1.704 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXDEV_2447refinement
xia20.3.8.0data scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: J30

Resolution: 1.46→70.51 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.34
RfactorNum. reflection% reflection
Rfree0.151 2000 1.49 %
Rwork0.14 --
obs0.14 134282 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.68 Å2
Refinement stepCycle: LAST / Resolution: 1.46→70.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 38 799 5092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074586
X-RAY DIFFRACTIONf_angle_d0.9246264
X-RAY DIFFRACTIONf_dihedral_angle_d16.3641669
X-RAY DIFFRACTIONf_chiral_restr0.076646
X-RAY DIFFRACTIONf_plane_restr0.007842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.49650.24981390.22819231X-RAY DIFFRACTION99
1.4965-1.5370.20811400.20479222X-RAY DIFFRACTION99
1.537-1.58220.16871400.18759261X-RAY DIFFRACTION99
1.5822-1.63330.2071400.17219263X-RAY DIFFRACTION99
1.6333-1.69170.18791410.1589338X-RAY DIFFRACTION99
1.6917-1.75940.19451410.14819321X-RAY DIFFRACTION100
1.7594-1.83950.14981420.13919351X-RAY DIFFRACTION100
1.8395-1.93650.13671420.13199409X-RAY DIFFRACTION100
1.9365-2.05780.15151430.12939413X-RAY DIFFRACTION100
2.0578-2.21670.13121420.12279477X-RAY DIFFRACTION100
2.2167-2.43980.13551440.11799494X-RAY DIFFRACTION100
2.4398-2.79280.16261440.12389573X-RAY DIFFRACTION100
2.7928-3.51870.12951480.12729716X-RAY DIFFRACTION100
3.5187-70.59420.1381540.144810213X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.5623 Å / Origin y: 33.1542 Å / Origin z: -12.5824 Å
111213212223313233
T0.0506 Å2-0.0104 Å2-0.0014 Å2-0.116 Å2-0.0018 Å2--0.1053 Å2
L0.4574 °2-0.0387 °20.1409 °2-0.4282 °2-0.1762 °2--0.6409 °2
S-0.0056 Å °-0.0294 Å °-0.0555 Å °-0.0432 Å °0.0177 Å °-0.0165 Å °0.0396 Å °-0.0145 Å °0.0074 Å °
Refinement TLS groupSelection details: ALL

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