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- PDB-4h7m: The X-ray Crystal Structure of the Trichoderma harzianum Endogluc... -

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Basic information

Entry
Database: PDB / ID: 4h7m
TitleThe X-ray Crystal Structure of the Trichoderma harzianum Endoglucanase 3 from family GH12
ComponentsEndo-1,4-beta-glucanase
KeywordsHYDROLASE / endoglucanase / GH12
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 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesTrichoderma harzianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.068 Å
AuthorsLiberato, M.V. / Polikarpov, I.
CitationJournal: Plos One / Year: 2013
Title: X-ray Structure and Molecular Dynamics Simulations of Endoglucanase 3 from Trichoderma harzianum: Structural Organization and Substrate Recognition by Endoglucanases That Lack Cellulose Binding Module.
Authors: Prates, E.T. / Stankovic, I. / Silveira, R.L. / Liberato, M.V. / Henrique-Silva, F. / Pereira, N. / Polikarpov, I. / Skaf, M.S.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-glucanase
B: Endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)49,1332
Polymers49,1332
Non-polymers00
Water5,657314
1
A: Endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)24,5671
Polymers24,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-glucanase


Theoretical massNumber of molelcules
Total (without water)24,5671
Polymers24,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.542, 55.569, 157.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24566.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma harzianum (fungus) / Strain: IOC-3844 / Gene: Egl3 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): MutS / References: UniProt: I3RY46, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Sodium chloride, 12 %(w/v) PEG 6000, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 26039 / % possible obs: 99.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.113 / Χ2: 1.002 / Net I/σ(I): 23.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.146.30.19924871.057197.5
2.14-2.236.40.18725100.995197.5
2.23-2.336.30.17725340.998198.6
2.33-2.456.40.16425481.04198.5
2.45-2.616.50.15525890.965199.3
2.61-2.816.70.14326140.9711100
2.81-3.096.90.1326171.0151100
3.09-3.5470.11926340.9581100
3.54-4.4670.10326681.0291100
4.46-506.70.0728380.998199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.06 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.51 Å
Translation2.5 Å45.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.068→45.508 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8598 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2238 1319 5.08 %
Rwork0.1825 --
obs0.1847 25975 98.94 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.52 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 65.14 Å2 / Biso mean: 20.8442 Å2 / Biso min: 2.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.0274 Å2-0 Å20 Å2
2---2.6411 Å20 Å2
3----0.3863 Å2
Refinement stepCycle: LAST / Resolution: 2.068→45.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 0 314 3783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073599
X-RAY DIFFRACTIONf_angle_d1.0394927
X-RAY DIFFRACTIONf_chiral_restr0.076511
X-RAY DIFFRACTIONf_plane_restr0.004645
X-RAY DIFFRACTIONf_dihedral_angle_d13.9641202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0685-2.15130.25351220.19812601272395
2.1513-2.24920.22861470.1962651279898
2.2492-2.36780.24481360.18722692282899
2.3678-2.51610.26881480.18552703285199
2.5161-2.71040.23161350.192427452880100
2.7104-2.98310.24461480.203727392887100
2.9831-3.41460.2621680.19127712939100
3.4146-4.30150.17411560.156328132969100
4.3015-45.51890.19871590.175229413100100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42520.2843-0.00520.7152-0.22540.09830.04830.0129-0.00380.2158-0.0926-0.1094-0.0448-0.0507-0.00520.0592-0.0123-0.00940.05030.00020.03825.2565-0.4733-27.7358
20.21920.0828-0.07170.6994-0.08230.41760.0184-0.0186-0.01310.06670.08490.11380.0123-0.01260.12070.0729-0.01090.02180.07390.00690.0858-12.03421.7983-11.8909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 226
2X-RAY DIFFRACTION2chain BB1 - 225

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