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- PDB-3ziz: Crystal structure of Podospora anserina GH5 beta-(1,4)-mannanase -

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Basic information

Entry
Database: PDB / ID: 3ziz
TitleCrystal structure of Podospora anserina GH5 beta-(1,4)-mannanase
ComponentsGH5 ENDO-BETA-1,4-MANNANASE
KeywordsHYDROLASE / MANNANASE / GLYCOSYL HYDROLASE / CAZY
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / 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 / Mannan endo-1,4-beta-mannosidase A
Similarity search - Component
Biological speciesPODOSPORA ANSERINA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCouturier, M. / Roussel, A. / Rosengren, A. / Leone, P. / Stalbrand, H. / Berrin, J.G.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Biochemical Analyses of Glycoside Hydrolase Families 5 and 26 Beta-(1,4)-Mannanases from Podospora Anserina Reveal Differences Upon Manno-Oligosaccharides Catalysis.
Authors: Couturier, M. / Roussel, A. / Rosengren, A. / Leone, P. / Stalbrand, H. / Berrin, J.G.
History
DepositionJan 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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: GH5 ENDO-BETA-1,4-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7113
Polymers42,4971
Non-polymers2142
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.870, 57.900, 97.860
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 GH5 ENDO-BETA-1,4-MANNANASE / BETA-1 / 4-MANNANASE


Mass: 42496.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PODOSPORA ANSERINA (fungus) / Strain: S MAT / Plasmid: PPICZAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33
References: UniProt: E2GHW1, UniProt: B2B3C0*PLUS, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / 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.: 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.5
Details: TRIS 0.1M PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97914
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 62519 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 10.99 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNO

1qno


Resolution: 1.4→28.95 Å / Cor.coef. Fo:Fc: 0.9657 / Cor.coef. Fo:Fc free: 0.9576 / SU R Cruickshank DPI: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.055
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3118. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3118. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=75.
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 3167 5.07 %RANDOM
Rwork0.1499 ---
obs0.151 62421 97.01 %-
Displacement parametersBiso mean: 13.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.3471 Å20 Å20 Å2
2--0.864 Å20 Å2
3----0.5169 Å2
Refine analyzeLuzzati coordinate error obs: 0.126 Å
Refinement stepCycle: LAST / Resolution: 1.4→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 14 434 3173
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012840HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.023869HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d949SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes424HARMONIC5
X-RAY DIFFRACTIONt_it2840HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.47
X-RAY DIFFRACTIONt_other_torsion15.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion355SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3686SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2526 228 5.13 %
Rwork0.1993 4214 -
all0.2019 4442 -
obs--97.01 %

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