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- PDB-1gvy: Substrate distorsion by beta-mannanase from Pseudomonas cellulosa -

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Basic information

Entry
Database: PDB / ID: 1gvy
TitleSubstrate distorsion by beta-mannanase from Pseudomonas cellulosa
ComponentsMANNAN ENDO-1,4-BETA-MANNOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GLYCOSIDASE / MANNANASE / MANNAN / FAMILY 26
Function / homology
Function and homology information


glucomannan metabolic process / galactomannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DINITROPHENYLENE / Mannan endo-1,4-beta-mannosidase
Similarity search - Component
Biological speciesPSEUDOMONAS CELLULOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDucros, V. / Zechel, D.L. / Gilbert, H.J. / Szabo, L. / Withers, S.G. / Davies, G.J.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2002
Title: Substrate Distortion by a Beta-Mannanase: Snapshots of the Michaelis and Covalent-Intermediate Complexes Suggest a B2,5 Conformation for the Transition State
Authors: Ducros, V. / Zechel, D.L. / Murshudov, G. / Gilbert, H.J. / Szabo, L. / Stoll, D. / Withers, S.G. / Davies, G.J.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of Mannanase 26A from Pseudomomnas Cellulosa and Analysis of Residues Involved in Substrate Binding
Authors: Hogg, D. / Woo, E.J. / Bolam, D.N. / Mckie, V.A. / Gilbert, H.J. / Pickersgill, R.W.
History
DepositionFeb 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2002Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,4038
Polymers43,3301
Non-polymers1,0737
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.192, 93.192, 54.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein MANNAN ENDO-1,4-BETA-MANNOSIDASE / BETA-MANNANASE / MANNANASE A


Mass: 43330.105 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH 2,4-DINITROPHENYL 2-DEOXY-2-FLUORO-BETA-MANNOTRIOSIDE
Source: (gene. exp.) PSEUDOMONAS CELLULOSA (bacteria) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P49424, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-deoxy-2-fluoro-beta-D-mannopyranose


Type: oligosaccharide / Mass: 506.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1122h-1b_1-5_2*F][a1122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp2fluoro]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 457 molecules

#3: Chemical ChemComp-NIN / DINITROPHENYLENE


Mass: 168.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N2O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE IN SWISS-PROT ENTRY P49424 IS INCORRECT (AS OF THE DATE OF RELEASE OF THIS ENTRY). SEE ...THE SEQUENCE IN SWISS-PROT ENTRY P49424 IS INCORRECT (AS OF THE DATE OF RELEASE OF THIS ENTRY). SEE J.BIOL.CHEM. (276) 31186, 2001.

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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: 2.69 Å3/Da / Density % sol: 53.86 %
Crystal growpH: 7.5 / Details: 100MM TRIS PH7.5, 26% PEG550, 9MM ZNSO4, pH 7.50
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop / Details: Hogg, D., (2001) J.Biol.Chem., 276, 31186.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 %PEG550 MME1reservoir
20.012 Mzinc sulfate1reservoir
30.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 50905 / % possible obs: 99.4 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.37
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.57 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.75 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J9Y

1j9y


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.968 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BREAK IN THE CHAIN A FROM RESIDUE 370 TO RESIDUE 372 DUE TO DISORDER IN THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2609 5.1 %RANDOM
Rwork0.144 ---
obs0.145 48658 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 65 451 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213177
X-RAY DIFFRACTIONr_bond_other_d0.0020.022715
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7231.9354339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.99536304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023551
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02676
X-RAY DIFFRACTIONr_nbd_refined0.2260.3717
X-RAY DIFFRACTIONr_nbd_other0.20.32701
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.4960.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.5338
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1050.53
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.510
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.520
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9571.51880
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56723039
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.26231297
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5674.51300
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.193 194
Rwork0.153 3456

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