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- PDB-1bqc: BETA-MANNANASE FROM THERMOMONOSPORA FUSCA -

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Basic information

Entry
Database: PDB / ID: 1bqc
TitleBETA-MANNANASE FROM THERMOMONOSPORA FUSCA
ComponentsPROTEIN (BETA-MANNANASE)
KeywordsHYDROLASE / MANNANASE / GLYCOSYL HYDROLASE / FAMILY 5 / THERMOMONOSPORA FUSCA
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
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsHilge, M. / Gloor, S.M. / Piontek, K.
CitationJournal: Structure / Year: 1998
Title: High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
Authors: Hilge, M. / Gloor, S.M. / Rypniewski, W. / Sauer, O. / Heightman, T.D. / Zimmermann, W. / Winterhalter, K. / Piontek, K.
History
DepositionAug 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
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: PROTEIN (BETA-MANNANASE)


Theoretical massNumber of molelcules
Total (without water)33,1231
Polymers33,1231
Non-polymers00
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.702, 46.058, 132.511
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 PROTEIN (BETA-MANNANASE)


Mass: 33123.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Source: (natural) Thermobifida fusca (bacteria) / Strain: KW3
References: UniProt: Q9ZF13, mannan endo-1,4-beta-mannosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growpH: 7 / Details: 1.85M AMMONIUM SULFATE, 0.1M HEPES, PH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.85 Mammonium sulfate1reservoir
20.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9072
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9072 Å / Relative weight: 1
ReflectionResolution: 1.5→32 Å / Num. obs: 42667 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.22 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 17.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.331 / % possible all: 92.2
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
WARPmodel building
REFMACrefinement
ARP/wARPmodel building
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→32 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: INDIVIDUAL, ANISOTROPIC B-FACTOR REFINEMENT USING REFMAC 4.0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2146 5 %RANDOM
Rwork0.119 ---
obs-42667 97.2 %-
Displacement parametersBiso mean: 15.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 434 2770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.022
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.119
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.5 Å2

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