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- PDB-3pzm: Structure of the hyperthermostable endo-1,4-beta-D-mannanase from... -

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Basic information

Entry
Database: PDB / ID: 3pzm
TitleStructure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 with three glycerol molecules
ComponentsMannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
KeywordsHYDROLASE / alpha/beta barrel / glycosyl hydrolase / sugar binding / secreted
Function / homology
Function and homology information


mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process / extracellular region
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 RKU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6125
Polymers44,2131
Non-polymers3984
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.458, 83.280, 91.960
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 RKU-1 (bacteria) / Strain: RKU-1 / Gene: Tpet_1542 / Production host: Escherichia coli (E. coli)
References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
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 10, 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: 1.5→41.3 Å / Num. all: 131640 / Num. obs: 68874 / % possible obs: 100 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→41.3 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.086 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17464 3474 5.1 %RANDOM
Rwork0.13121 ---
obs0.1334 65092 99.58 %-
all-65092 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 26 363 3316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223056
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.9364139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89823.988163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58315491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8391517
X-RAY DIFFRACTIONr_chiral_restr0.1660.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212400
X-RAY DIFFRACTIONr_mcbond_it2.4751.51773
X-RAY DIFFRACTIONr_mcangle_it3.38122851
X-RAY DIFFRACTIONr_scbond_it4.55931283
X-RAY DIFFRACTIONr_scangle_it6.0624.51288
X-RAY DIFFRACTIONr_rigid_bond_restr2.73633056
X-RAY DIFFRACTIONr_sphericity_free12.5063363
X-RAY DIFFRACTIONr_sphericity_bonded7.45432970
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 288 -
Rwork0.242 4698 -
obs--98.77 %

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