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- PDB-1qns: The 3-D structure of a Trichoderma reesei b-mannanase from glycos... -

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Basic information

Entry
Database: PDB / ID: 1qns
TitleThe 3-D structure of a Trichoderma reesei b-mannanase from glycoside hydrolase family 5
ComponentsENDO-1,4-B-D-MANNANASE
KeywordsHYDROLASE / MANNANASE / ANOMALOUS SCATTERING
Function / homology
Function and homology information


mannan catabolic process / disaccharide binding / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / cellulose binding / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases ...Mannan endo-1,4-beta-mannosidase-like / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase, family 5 / 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 A
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsSabini, E. / Schubert, H. / Murshudov, G. / Wilson, K.S. / Siika-Aho, M. / Penttila, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The Three-Dimensional Structure of a Trichoderma Reesei Beta-Mannanase from Glycoside Hydrolase Family 5
Authors: Sabini, E. / Schubert, H. / Murshudov, G. / Wilson, K.S. / Siika-Aho, M. / Penttila, M.
History
DepositionOct 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-B-D-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,12610
Polymers37,7471
Non-polymers1,3799
Water8,233457
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.180, 54.600, 60.760
Angle α, β, γ (deg.)90.00, 111.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein ENDO-1,4-B-D-MANNANASE


Mass: 37747.137 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 28-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Strain: ALKO4330 / Cellular location (production host): SECRETED / Gene (production host): CBH1 PROMOTER / Production host: TRICHODERMA REESEI (fungus) / Strain (production host): ALKO4330
References: UniProt: Q99036, mannan endo-1,4-beta-mannosidase
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 462 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growpH: 8.5 / Details: 2M AMMONIUM SULPHATE 0.1M TRIS-HCL PH 8.5
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlenzyme1drop
210 mMTris-HCl1drop
32 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 40304 / % possible obs: 84.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 10.334 Å2 / Rsym value: 0.042 / Net I/σ(I): 22.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 8.4 / % possible all: 52.4
Reflection
*PLUS
Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 52.4 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.5→20 Å / SU B: 0.91031 / SU ML: 0.03482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.0754 / ESU R Free: 0.06391
RfactorNum. reflection% reflectionSelection details
Rfree0.157 -5 %RANDOM
Rwork0.111 ---
obs-60810 84.1 %-
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.242 Å20 Å20.55 Å2
2--0.282 Å20 Å2
3----0.031 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 87 457 3213
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.082
X-RAY DIFFRACTIONp_mcangle_it2.773
X-RAY DIFFRACTIONp_scbond_it2.4472
X-RAY DIFFRACTIONp_scangle_it3.2163
X-RAY DIFFRACTIONp_plane_restr0.0269
X-RAY DIFFRACTIONp_chiral_restr0.1140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1660.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor57
X-RAY DIFFRACTIONp_staggered_tor11.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.720
X-RAY DIFFRACTIONp_special_tor15

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