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- PDB-2bw8: Native structure of Endoglucanase 12A (Cel12A) from Rhodothermus ... -

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Basic information

Entry
Database: PDB / ID: 2bw8
TitleNative structure of Endoglucanase 12A (Cel12A) from Rhodothermus marinus
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / ENDOGLUCANASE / CELLULASE / GLYCOSIDE HYDROLASE FAMILY 12
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsCrennell, S.J. / Nordberg-Karlsson, E.
CitationJournal: J. Mol. Biol. / Year: 2006
Title: Dimerisation and an increase in active site aromatic groups as adaptations to high temperatures: X-ray solution scattering and substrate-bound crystal structures of Rhodothermus marinus endoglucanase Cel12A.
Authors: Crennell, S.J. / Cook, D. / Minns, A. / Svergun, D. / Andersen, R.L. / Nordberg Karlsson, E.
History
DepositionJul 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE
B: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5203
Polymers50,4242
Non-polymers961
Water7,188399
1
A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3082
Polymers25,2121
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDOGLUCANASE


Theoretical massNumber of molelcules
Total (without water)25,2121
Polymers25,2121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.283, 67.867, 132.458
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


Mass: 25211.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Strain: ITI-378
Description: MARINE THERMOPHILIC EUBACTERIUM ISOLATED FROM ALKALINE SUBMARINE HOT SPRINGS
Plasmid: (SP, L)CEL12A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O33897, cellulase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE BETWEEN RESIDUES 69 AND 93 IN THE DBREF RECORDS BELOW REPRESENT ...THE AUTHORS STATE THAT THE SEQUENCE BETWEEN RESIDUES 69 AND 93 IN THE DBREF RECORDS BELOW REPRESENT THE TRUE SEQUENCE OF THE PROTEIN. THE CORRESPONDING UNIPROT CONTAINS THE RESULTS OF A SEQUENCING ERROR DISCOVERED DURING THE PREVIOUS DETERMINATION OF THE STRUCTURE (PDB ENTRY 1H0B).

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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: 2.5 Å3/Da / Density % sol: 41.5 %
Crystal growpH: 6.5
Details: 0.1M MES PH 6.5, 1.5M (NH4)2SO4, 0.2M LI2SO4, 10MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97845
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 25, 2003 / Details: MIRRORS
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.54→23 Å / Num. obs: 75552 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.6
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOB

1hob


Resolution: 1.54→22.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1663021.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.18 3773 5 %RANDOM
Rwork0.157 ---
obs0.157 75468 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0957 Å2 / ksol: 0.328731 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.56 Å20 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.54→22.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 5 399 3952
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it3.242
X-RAY DIFFRACTIONc_scbond_it3.842
X-RAY DIFFRACTIONc_scangle_it5.682.5
LS refinement shellResolution: 1.54→1.64 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 584 4.7 %
Rwork0.218 11833 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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