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- PDB-1rh9: Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato) -

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Basic information

Entry
Database: PDB / ID: 1rh9
TitleFamily GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato)
Componentsendo-beta-mannanase
KeywordsHYDROLASE / ENDO-BETA-MANNASE / Retaining / Glycoside Hydrolase Family 5 / mannan
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Mannan endo-1,4-beta-mannosidase 4 / Mannan endo-1,4-beta-mannosidase 4
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOakley, A.J. / Bourgault, R. / Bewley, J.D. / Wilce, M.C.J.
CitationJournal: Protein Sci. / Year: 2005
Title: Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.
Authors: Bourgault, R. / Oakley, A.J. / Bewley, J.D. / Wilce, M.C.
History
DepositionNov 14, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endo-beta-mannanase


Theoretical massNumber of molelcules
Total (without water)42,4361
Polymers42,4361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.540, 74.521, 79.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains the biological assembly (a monomer).

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Components

#1: Protein endo-beta-mannanase


Mass: 42435.910 Da / Num. of mol.: 1 / Fragment: residues 27-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: LeMAN4a / Plasmid: pMAL-c2X / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
References: UniProt: Q93WT4, UniProt: Q8L5J1*PLUS, mannan endo-1,4-beta-mannosidase
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: 1.99 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1M Na Citrate, 0.2M NH4 Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2003 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→54.233 Å / Num. all: 56178 / Num. obs: 56178 / % possible obs: 98.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QNP

1qnp


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.977 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.084 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20479 2853 5.1 %RANDOM
Rwork0.18248 ---
all0.18364 53236 --
obs0.18364 53236 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 0 0 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223240
X-RAY DIFFRACTIONr_bond_other_d0.0020.022801
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9274413
X-RAY DIFFRACTIONr_angle_other_deg0.78136564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235405
X-RAY DIFFRACTIONr_chiral_restr0.0740.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023694
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02687
X-RAY DIFFRACTIONr_nbd_refined0.2210.2698
X-RAY DIFFRACTIONr_nbd_other0.2370.23379
X-RAY DIFFRACTIONr_nbtor_other0.1030.21767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.236
X-RAY DIFFRACTIONr_mcbond_it0.5911.51957
X-RAY DIFFRACTIONr_mcangle_it1.08423179
X-RAY DIFFRACTIONr_scbond_it1.60631283
X-RAY DIFFRACTIONr_scangle_it2.5714.51234
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 200
Rwork0.308 3906

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