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- PDB-1vjz: Crystal structure of Endoglucanase (TM1752) from Thermotoga marit... -

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Basic information

Entry
Database: PDB / ID: 1vjz
TitleCrystal structure of Endoglucanase (TM1752) from Thermotoga maritima at 2.05 A resolution
Componentsendoglucanase
KeywordsENDOGLUCANASE / TM1752 / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Endoglucanase (TM1752) from Thermotoga maritima at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endoglucanase


Theoretical massNumber of molelcules
Total (without water)41,0971
Polymers41,0971
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.684, 64.684, 202.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein endoglucanase


Mass: 41096.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1752 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X274, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5351.06
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop9Bicine pH 9, 2% Dioxane, 10% PEG-20000, pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop9Bicine pH 9, 2% Dioxane, 10% PEG-20000, pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-BM10.980502
SYNCHROTRONAPS 19-BM20.964063, 0.979292
Detector
TypeIDDetectorDateDetails
APS-11CCDFeb 20, 2004water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
APS-12CCDFeb 20, 2004water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
2Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9805021
20.9640631
30.9792921
ReflectionResolution: 2.05→50 Å / Num. obs: 26538 / % possible obs: 94.64 % / Redundancy: 3.82 % / Biso Wilson estimate: 34.42 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.57
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.75 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3 / Num. unique all: 2053 / % possible all: 75.23

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→32.34 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.85 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.21244 1336 5 %RANDOM
Rwork0.16804 ---
obs0.17021 25186 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.751 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 0 212 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222861
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9123884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61323.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48815491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0871519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022211
X-RAY DIFFRACTIONr_nbd_refined0.1980.21368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.25
X-RAY DIFFRACTIONr_mcbond_it2.07531678
X-RAY DIFFRACTIONr_mcangle_it2.96752662
X-RAY DIFFRACTIONr_scbond_it5.47381398
X-RAY DIFFRACTIONr_scangle_it7.209111222
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 69 4.68 %
Rwork0.195 1405 -
Refinement TLS params.Method: refined / Origin x: 7.864 Å / Origin y: 26.646 Å / Origin z: 47.722 Å
111213212223313233
T0.0505 Å2-0.0335 Å20.0072 Å2-0.0212 Å20.0157 Å2--0.0761 Å2
L0.5077 °20.1897 °2-0.3738 °2-0.6271 °2-0.7043 °2--3.6131 °2
S-0.0493 Å °-0.0042 Å °-0.0197 Å °-0.0303 Å °0.0039 Å °-0.0145 Å °0.2778 Å °-0.0023 Å °0.0454 Å °
Refinement TLS groupSelection: ALL

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