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- PDB-6kdd: endoglucanase -

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Basic information

Entry
Database: PDB / ID: 6kdd
Titleendoglucanase
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / endoglucanase
Function / homology
Function and homology information


organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Endoglucanase
Similarity search - Component
Biological speciesFervidobacterium pennivorans DSM 9078 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYu, S. / Liuqing, C.
CitationJournal: To Be Published
Title: crystal structure of an endoglucanase from Fervidobacterium pennivorans DSM9078
Authors: Yu, S.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)38,4847
Polymers37,9391
Non-polymers5466
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.138, 54.895, 128.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase / Cellulase


Mass: 37938.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium pennivorans DSM 9078 (bacteria)
Strain: DSM 9078 / Ven5 / Gene: Ferpe_1841 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9UEE9
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 27732 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.985 / Rpim(I) all: 0.034 / Rrim(I) all: 0.105 / Net I/σ(I): 4
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2715 / CC1/2: 0.967 / Rpim(I) all: 0.149 / Rrim(I) all: 0.474 / Χ2: 1.004 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→41.73 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.212 1381 5 %
Rwork0.201 --
obs-27675 95 %
Refinement stepCycle: LAST / Resolution: 1.92→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 30 101 2718
LS refinement shellResolution: 1.92→1.99 Å
RfactorNum. reflection% reflection
Rfree0.262 121 -
Rwork0.258 2579 -
obs--99.3 %

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