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- PDB-6vc5: 1.6 Angstrom Resolution Crystal Structure of endoglucanase from K... -

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Basic information

Entry
Database: PDB / ID: 6vc5
Title1.6 Angstrom Resolution Crystal Structure of endoglucanase from Komagataeibacter sucrofermentans
ComponentsEndoglucanase
KeywordsHYDROLASE / endoglucanase
Function / homologyGlycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / cellulase / cellulase activity / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / cellulase
Function and homology information
Biological speciesKomagataeibacter sucrofermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWu, R. / Kim, Y. / Jedrzrjczak, R. / Joachimiak, A.
CitationJournal: To Be Published
Title: 1.6 Angstrom Resolution Crystal Structure of endoglucanase from Komagataeibacter sucrofermentans
Authors: Wu, R. / Kim, Y. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8985
Polymers35,5291
Non-polymers3684
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.520, 120.520, 47.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Endoglucanase


Mass: 35529.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataeibacter sucrofermentans (bacteria)
Gene: CMCase / Plasmid: PLASMID / Details (production host): pMCSG53 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: O82857
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.6M NaCl, 0.1M MES.NaOH, pH6.5, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.495→50 Å / Num. obs: 55405 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 12.13 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.044 / Rrim(I) all: 0.103 / Χ2: 0.833 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.533.11.30627440.2160.8341.5570.88699.3
1.53-1.553.51.37327410.260.8271.610.9499.6
1.55-1.5841.39627600.310.7821.6070.92399.7
1.58-1.624.51.48827490.3070.7811.6870.90899.9
1.62-1.6551.30127320.5050.6471.4580.91399.9
1.65-1.694.91.12227850.5540.5581.2570.92799.9
1.69-1.735.20.96527190.6360.4721.0770.922100
1.73-1.785.60.72427930.7950.340.8010.952100
1.78-1.835.60.55627460.8620.2610.6160.945100
1.83-1.895.50.4127810.9030.1940.4550.94199.9
1.89-1.965.30.28627460.9450.1370.3180.944100
1.96-2.0450.20327520.9570.1010.2270.93799.5
2.04-2.135.60.15827740.9780.0730.1740.85999.9
2.13-2.245.70.11627510.9840.0540.1280.793100
2.24-2.385.60.09128010.9880.0420.10.71499.9
2.38-2.565.40.07727630.9880.0360.0860.715100
2.56-2.825.50.06727840.9910.0310.0740.691100
2.82-3.235.80.06227940.9930.0280.0680.696100
3.23-4.075.30.05628160.9940.0260.0620.6899.7
4.07-505.60.05628740.9910.0250.0620.57299.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1309refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wzz

1wzz


Resolution: 1.5→38.112 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.32
RfactorNum. reflection% reflection
Rfree0.1756 2465 4.95 %
Rwork0.1553 --
obs0.1564 49781 89.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.85 Å2 / Biso mean: 16.1254 Å2 / Biso min: 3.91 Å2
Refinement stepCycle: final / Resolution: 1.5→38.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 24 377 2898
Biso mean--31.42 31.72 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082643
X-RAY DIFFRACTIONf_angle_d1.0793608
X-RAY DIFFRACTIONf_chiral_restr0.085377
X-RAY DIFFRACTIONf_plane_restr0.007460
X-RAY DIFFRACTIONf_dihedral_angle_d21.731922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.52360.3128400.241661621
1.5236-1.55470.2337630.1901137648
1.5547-1.58850.22321210.1811216974
1.5885-1.62550.22671210.1737254588
1.6255-1.66610.21131230.1659273293
1.6661-1.71120.20021420.1591274895
1.7112-1.76150.18891650.1527288499
1.7615-1.81840.18831610.1489285399
1.8184-1.88340.17941580.14282930100
1.8834-1.95880.18471710.13642862100
1.9588-2.04790.16631580.135291599
2.0479-2.15590.17451200.14132968100
2.1559-2.29090.14461570.14152896100
2.2909-2.46780.17611440.15072950100
2.4678-2.71610.19231650.16612919100
2.7161-3.10890.17241520.16392956100
3.1089-3.91630.16741460.15482966100
3.9163-38.1120.15661580.1623031100

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