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- PDB-1ksd: The structure of Endoglucanase from termite, Nasutitermes takasag... -

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Basic information

Entry
Database: PDB / ID: 1ksd
TitleThe structure of Endoglucanase from termite, Nasutitermes takasagoensis, at pH 6.5.
ComponentsEndo-b-1,4-glucanase
KeywordsHYDROLASE / Cellulase / Endoglucanase / Termite / Nasutitermes takasagoensis / Glycosyl Hydrolase / Family 9 / (Alpha/Alpha)6
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Biological speciesNasutitermes takasagoensis (cockroach)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKhademi, S. / Guarino, L.A. / Watanabe, H. / Tokuda, G. / Meyer, E.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of an endoglucanase from termite, Nasutitermes takasagoensis.
Authors: Khademi, S. / Guarino, L.A. / Watanabe, H. / Tokuda, G. / Meyer, E.F.
History
DepositionJan 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-b-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8842
Polymers47,8441
Non-polymers401
Water12,701705
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.251, 83.924, 60.878
Angle α, β, γ (deg.)90.00, 95.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endo-b-1,4-glucanase


Mass: 47844.309 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nasutitermes takasagoensis (cockroach) / Plasmid: pET3a-Nts / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O77044, cellulase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, Sodium Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5
Crystal grow
*PLUS
pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.1 Mprotein1droppH4.5
30.8 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030K / Detector: IMAGE PLATE / Date: Jun 1, 2000 / Details: mirrors
RadiationMonochromator: OSMIC, Model 140-000023 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 58967 / Num. obs: 57195 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 19.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.6
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.6 / % possible all: 92.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 654717
Reflection shell
*PLUS
% possible obs: 92.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TF4

3tf4


Resolution: 1.6→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 5717 9.7 %RANDOM
Rwork0.17 ---
all-58848 --
obs-57085 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2325 Å2 / ksol: 0.378856 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.23 Å20 Å21.64 Å2
2---2.34 Å20 Å2
3----2.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 1 705 4089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.362
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.269 553 10.2 %
Rwork0.241 4864 -
obs-5417 92.4 %
Xplor fileSerial no: 1 / Param file: protein-rep.param / Topol file: protein.top
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.201 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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