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- PDB-3ik2: Crystal Structure of a Glycoside Hydrolase Family 44 Endoglucanas... -

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Basic information

Entry
Database: PDB / ID: 3ik2
TitleCrystal Structure of a Glycoside Hydrolase Family 44 Endoglucanase produced by Clostridium acetobutylium ATCC 824
ComponentsEndoglucanase A
KeywordsHYDROLASE / TIM-like barrel
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / EF-Hand 1, calcium-binding site ...Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Endoglucanase A (Endo-1,4-beta-glucanase) (Cellulase A), secreted dockerin domain
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWarner, C.D. / Hoy, J.A. / Ford, C.F. / Honzatko, R.B. / Reilly, P.J.
CitationJournal: Appl.Environ.Microbiol. / Year: 2010
Title: Tertiary structure and characterization of a glycoside hydrolase family 44 endoglucanase from Clostridium acetobutylicum.
Authors: Warner, C.D. / Hoy, J.A. / Shilling, T.C. / Linnen, M.J. / Ginder, N.D. / Ford, C.F. / Honzatko, R.B. / Reilly, P.J.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,89117
Polymers57,6541
Non-polymers1,23716
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.078, 87.285, 103.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endoglucanase A / Endo-1 / 4-beta-glucanase / Cellulase A


Mass: 57653.953 Da / Num. of mol.: 1
Fragment: UNP RESIDUES 34-541(Fragment excluding signal peptide & dockerin domain)
Source method: isolated from a genetically manipulated source
Details: Gene synthesized by Megabase (Lincoln, NE) / Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CAC0915, CA_C0915 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q977Y3

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Non-polymers , 6 types, 653 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.2 M (NH4)2SO4, 0.1 M NaOAc, 10% (w/v) PEG 3,350, pH 5.4, vapor diffusion, hanging drop, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 28, 2007
RadiationMonochromator: Tuned to copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→66.67 Å / Num. all: 25388 / Num. obs: 25388 / % possible obs: 99.5 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 4.87 % / Rmerge(I) obs: 0.086 / Χ2: 0.96 / Net I/σ(I): 11.4 / Scaling rejects: 935
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.19 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5 / Num. measured all: 9990 / Num. unique all: 2363 / Χ2: 1.34 / % possible all: 94.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E4T.pdb

2e4t


Resolution: 2.2→66.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.814 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 2 / ESU R: 0.326 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1260 5 %RANDOM
Rwork0.151 ---
all0.166 25388 --
obs0.155 25324 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 243.86 Å2 / Biso mean: 13.764 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2--0.95 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 77 637 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224187
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9395678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77325.644202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82615646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.953158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023284
X-RAY DIFFRACTIONr_nbd_refined0.2130.22225
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2671
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.265
X-RAY DIFFRACTIONr_mcbond_it0.7061.52619
X-RAY DIFFRACTIONr_mcangle_it1.17224103
X-RAY DIFFRACTIONr_scbond_it1.99931855
X-RAY DIFFRACTIONr_scangle_it2.9324.51575
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 82 -
Rwork0.164 1634 -
all-1716 -
obs--92.21 %

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