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- PDB-3pz9: Native structure of endo-1,4-beta-D-mannanase from Thermotoga pet... -

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Basic information

Entry
Database: PDB / ID: 3pz9
TitleNative structure of endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1
ComponentsMannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
KeywordsHYDROLASE / alpha/beta-barrel / manosidase / carbohydrate/sugar binding / secreted
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / metabolic process
Similarity search - Function
Carbohydrate binding module 27 / Carbohydrate binding module 27 / Mannan endo-1,4-beta-mannosidase-like / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
Similarity search - Component
Biological speciesThermotoga petrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.42 Å
AuthorsSantos, C.R. / Meza, A.N. / Paiva, J.H. / Silva, J.C. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T.
CitationJournal: To be Published
Title: Structural characterization of a novel hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1
Authors: Santos, C.R. / Meza, A.N. / Paiva, J.H. / Silva, J.C. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5


Theoretical massNumber of molelcules
Total (without water)44,2131
Polymers44,2131
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.463, 83.352, 92.179
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 Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5


Mass: 44213.379 Da / Num. of mol.: 1 / Fragment: UNP residues 32-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila (bacteria) / Strain: RKU-1 / Gene: Tpet_1542 / Production host: Escherichia coli (E. coli)
References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.8 M phosphate, 0.2 M sodium chloride, pH 5.5, 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: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.42→40.33 Å / Num. obs: 80074 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.42→1.47 Å / % possible all: 86

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXmodel building
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.42→40.33 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.786 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17849 4002 5 %RANDOM
Rwork0.14545 ---
obs0.14714 79961 98.34 %-
all-79961 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.42→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 0 417 3344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0223034
X-RAY DIFFRACTIONr_angle_refined_deg2.2291.9294115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0945356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3423.889162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46115490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7771517
X-RAY DIFFRACTIONr_chiral_restr0.1750.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212398
X-RAY DIFFRACTIONr_mcbond_it2.7471.51769
X-RAY DIFFRACTIONr_mcangle_it3.7222845
X-RAY DIFFRACTIONr_scbond_it4.78731265
X-RAY DIFFRACTIONr_scangle_it6.3214.51270
X-RAY DIFFRACTIONr_rigid_bond_restr3.01133034
X-RAY DIFFRACTIONr_sphericity_free14.3133417
X-RAY DIFFRACTIONr_sphericity_bonded8.42532943
LS refinement shellResolution: 1.42→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.496 230 -
Rwork0.496 4707 -
obs--83.64 %

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