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

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Basic information

Entry
Database: PDB / ID: 3pzo
TitleStructure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with three maltose 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
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
alpha-maltose / Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5
Similarity search - Component
Biological speciesThermotoga petrophila RKU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,0825
Polymers44,2131
Non-polymers8694
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.293, 83.300, 92.082
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 / ATCC BAA-488 / DSM 13995 / Gene: Tpet_1542 / Production host: Escherichia coli (E. coli)
References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
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: Jul 11, 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: 1.55→40.3 Å / Num. obs: 59171 / % possible obs: 99.6 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.55→40.3 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.336 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20248 3072 5 %RANDOM
Rwork0.1703 ---
obs0.17191 57815 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.635 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 58 291 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0223092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5511.9514195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51723.988163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30415491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3111517
X-RAY DIFFRACTIONr_chiral_restr0.20.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4851.51769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26822845
X-RAY DIFFRACTIONr_scbond_it3.31631323
X-RAY DIFFRACTIONr_scangle_it5.0754.51350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 196 -
Rwork0.401 3541 -
obs--82.15 %

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