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- PDB-1vrx: Endocellulase e1 from acidothermus cellulolyticus mutant y245g -

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Basic information

Entry
Database: PDB / ID: 1vrx
TitleEndocellulase e1 from acidothermus cellulolyticus mutant y245g
ComponentsENDOCELLULASE E1 FROM A. CELLULOLYTICUS
KeywordsHYDROLASE / ALPHA/BETA BARREL / ENDO-1 / 4-BETA-D-GLUCANASE
Function / homology
Function and homology information


cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) ...Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcidothermus cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 2.4 Å
AuthorsBaker, J.O. / McCarley, J.R. / Lovett, R. / Yu, C.H. / Adney, W.S. / Rignall, T.R. / Vinzant, T.B. / Decker, S.R. / Sakon, J. / Himmel, M.E.
CitationJournal: Appl.Biochem.Biotechnol. / Year: 2005
Title: Catalytically enhanced endocellulase Cel5A from Acidothermus cellulolyticus.
Authors: Baker, J.O. / McCarley, J.R. / Lovett, R. / Yu, C.H. / Adney, W.S. / Rignall, T.R. / Vinzant, T.B. / Decker, S.R. / Sakon, J. / Himmel, M.E.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJul 5, 2005ID: 1C0D
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOCELLULASE E1 FROM A. CELLULOLYTICUS
B: ENDOCELLULASE E1 FROM A. CELLULOLYTICUS


Theoretical massNumber of molelcules
Total (without water)80,3492
Polymers80,3492
Non-polymers00
Water4,179232
1
A: ENDOCELLULASE E1 FROM A. CELLULOLYTICUS


Theoretical massNumber of molelcules
Total (without water)40,1741
Polymers40,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDOCELLULASE E1 FROM A. CELLULOLYTICUS


Theoretical massNumber of molelcules
Total (without water)40,1741
Polymers40,1741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.690, 96.690, 258.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21B-544-

HOH

DetailsThe biological assembly is a monomer.

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Components

#1: Protein ENDOCELLULASE E1 FROM A. CELLULOLYTICUS


Mass: 40174.477 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, BAMH1 FRAGMENT / Mutation: Y245G, V342D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidothermus cellulolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P54583, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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 Å3/Da / Density % sol: 71.66 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.2M NaCl 0.1M Sodium Citrate (pH4) 0.3M manoheptose, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→8 Å / Num. all: 53535 / Num. obs: 53535 / % possible obs: 89.5 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 1.2 / Redundancy: 1.99 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.74 / Num. unique all: 53535 / % possible all: 78

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Processing

Software
NameClassification
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 2.4→8 Å / Num. parameters: 2376 / Num. restraintsaints: 2395 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2644 5 %RANDOM
Rwork0.193 ---
all0.193 52895 --
obs0.193 50251 92.9 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5935
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5710 0 0 232 5942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.24
X-RAY DIFFRACTIONs_approx_iso_adps0

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