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- PDB-2c0h: X-ray structure of beta-mannanase from blue mussel Mytilus edulis -

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Basic information

Entry
Database: PDB / ID: 2c0h
TitleX-ray structure of beta-mannanase from blue mussel Mytilus edulis
ComponentsMANNAN ENDO-1,4-BETA-MANNOSIDASE
KeywordsHYDROLASE / MYTILUS EDULIS / TIM ALPHA/BETA BARREL
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity
Similarity search - Function
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
Similarity search - Component
Biological speciesMYTILUS EDULIS (blue mussel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLarsson, A.M. / Anderson, L. / Xu, B. / Munoz, I.G. / Uson, I. / Janson, J.-C. / Stalbrand, H. / Stahlberg, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Three-Dimensional Crystal Structure and Enzymic Characterization of Beta-Mannanase Man5A from Blue Mussel Mytilus Edulis.
Authors: Larsson, A.M. / Anderson, L. / Xu, B. / Munoz, I.G. / Uson, I. / Janson, J.-C. / Stalbrand, H. / Stahlberg, J.
History
DepositionSep 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANNAN ENDO-1,4-BETA-MANNOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6872
Polymers39,5911
Non-polymers961
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.073, 65.164, 93.086
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 / ENDO-BETA-1 / 4-D-MANNANASES / BETA-MANNANASE / MANA


Mass: 39590.859 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYTILUS EDULIS (blue mussel) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H
References: UniProt: Q8WPJ2, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 15 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 16 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 15 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 16 TO ALA ENGINEERED RESIDUE IN CHAIN A, ALA 17 TO VAL
Sequence detailsTHE CONFLICTS SHOWN IN THE SEQADV RECORDS BELOW ARE NOT INTENTIONAL MUTATIONS, AND THE AUTHORS ...THE CONFLICTS SHOWN IN THE SEQADV RECORDS BELOW ARE NOT INTENTIONAL MUTATIONS, AND THE AUTHORS CANNOT SAY WHETHER THIS IS AN ERROR IN THE CONSTRUCT OR IN THE ORIGINAL SEQUENCE.

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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: 2.3 Å3/Da / Density % sol: 44.9 %
Crystal growpH: 6.5
Details: 0.1 M MES PH6.5, 0.2 M AMMONIUM SULPHATE, 25%(W/V) MME PEG 5000, 3% DIOXANE, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2001 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→52.7 Å / Num. obs: 48523 / % possible obs: 98.5 % / Observed criterion σ(I): 6 / Redundancy: 5.4 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.9 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 1.6→19.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.42 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2426 5.1 %RANDOM
Rwork0.19 ---
obs0.191 45297 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 5 203 3000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212876
X-RAY DIFFRACTIONr_bond_other_d0.0010.022393
X-RAY DIFFRACTIONr_angle_refined_deg1.31.8973892
X-RAY DIFFRACTIONr_angle_other_deg0.84635578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54824.122148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4415453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0731513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
X-RAY DIFFRACTIONr_nbd_refined0.1980.2497
X-RAY DIFFRACTIONr_nbd_other0.1750.22144
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21380
X-RAY DIFFRACTIONr_nbtor_other0.080.21370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0361.52234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21422760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16231386
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0674.51132
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 125
Rwork0.196 2234

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