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- PDB-4cd7: The structure of GH113 beta-mannanase AaManA from Alicyclobacillu... -

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Basic information

Entry
Database: PDB / ID: 4cd7
TitleThe structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG and beta-1,4-mannobiose
ComponentsENDO-BETA-1,4-MANNANASE
KeywordsHYDROLASE / BETA-MANNOSIDASE / MANNOSIDASE / GLYCOSIDE HYDROLASE / GH26 / GH113 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / BIOCATALYSIS / CONFORMATION
Function / homology
Function and homology information


: / Glycoside Hydrolase Family 113 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Endo-beta-1,4-mannanase
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWilliams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate.
Authors: Williams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J.
History
DepositionOct 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,0258
Polymers72,6862
Non-polymers1,3396
Water8,467470
1
A: ENDO-BETA-1,4-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0134
Polymers36,3431
Non-polymers6703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-BETA-1,4-MANNANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0134
Polymers36,3431
Non-polymers6703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.472, 76.586, 140.212
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 ENDO-BETA-1,4-MANNANASE / AAMANA BETA-MANNANASE


Mass: 36342.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
Strain: TC-12-31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: A5H1I6, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#4: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.1 M SODIUM ACETATE PH 4.6, 4% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→76.59 Å / Num. obs: 88667 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / % possible all: 78.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
xia2IMPLEMENTATION OF XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CIV

3civ


Resolution: 1.65→70.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.143 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19617 4466 5.1 %RANDOM
Rwork0.15081 ---
obs0.15313 83793 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.621 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→70.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 88 470 5529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195298
X-RAY DIFFRACTIONr_bond_other_d0.0010.024647
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.947226
X-RAY DIFFRACTIONr_angle_other_deg1.03310731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68622.819259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60615768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5231540
X-RAY DIFFRACTIONr_chiral_restr0.1060.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021298
X-RAY DIFFRACTIONr_nbd_refined0.2440.21539
X-RAY DIFFRACTIONr_nbd_other0.1760.24257
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22534
X-RAY DIFFRACTIONr_nbtor_other0.0870.22652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0890.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.289
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9751.3582532
X-RAY DIFFRACTIONr_mcbond_other1.9751.3582533
X-RAY DIFFRACTIONr_mcangle_it2.3572.0433167
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7731.6252766
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3412.3474048
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.46639945
X-RAY DIFFRACTIONr_sphericity_free30.615137
X-RAY DIFFRACTIONr_sphericity_bonded8.839510105
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 262 -
Rwork0.209 4986 -
obs--79 %

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