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- PDB-1is9: Endoglucanase A from Clostridium thermocellum at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 1is9
TitleEndoglucanase A from Clostridium thermocellum at atomic resolution
Componentsendoglucanase A
KeywordsHYDROLASE / endoglucanase family 8 / Hg derivative
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily ...Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Alpha
Similarity search - Domain/homology
: / Endoglucanase A / Endoglucanase A
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.03 Å
AuthorsSchmidt, A. / Gonzalez, A. / Morris, R.J. / Costabel, M. / Alzari, P.M. / Lamzin, V.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Advantages of high-resolution phasing: MAD to atomic resolution.
Authors: Schmidt, A. / Gonzalez, A. / Morris, R.J. / Costabel, M. / Alzari, P.M. / Lamzin, V.S.
History
DepositionNov 26, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,79714
Polymers40,3451
Non-polymers1,45213
Water13,691760
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.441, 62.829, 103.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein endoglucanase A


Mass: 40345.277 Da / Num. of mol.: 1 / Fragment: residues 1-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P04955, UniProt: A3DC29*PLUS, cellulase
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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 Å3/Da / Density % sol: 38.47 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Details: macroseeding, Souchon, H., (1996) Proteins: Struct.,Funct., Genet., 25, 134.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris11pH7.5
20.2 M11NaCl
317 %PEG400011
40.1 MTris-HCl12pH7.2
515 %PEG800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.801, 1.008, 1.006
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8011
21.0081
31.0061
ReflectionResolution: 1→25 Å / Num. all: 158384 / Num. obs: 158384 / % possible obs: 97 % / Redundancy: 4 % / Biso Wilson estimate: 5.5 Å2 / Rsym value: 0.051 / Net I/σ(I): 14
Reflection shellResolution: 1.02→1.03 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.35 / % possible all: 91
Reflection
*PLUS
Highest resolution: 1.03 Å / Lowest resolution: 30 Å / Num. all: 304029 / % possible obs: 98.2 % / Num. measured all: 1605139 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 90.9 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.03→25 Å / Isotropic thermal model: anisotropic except solvent water / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.149 7920 5 %random
Rwork0.131 ---
all-158384 --
obs-158384 98 %-
Refinement stepCycle: LAST / Resolution: 1.03→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 13 760 3600
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.149 / Rfactor Rwork: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS

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