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- PDB-5xtt: Crystal structure of RmMan134A-M3 complex -

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Basic information

Entry
Database: PDB / ID: 5xtt
TitleCrystal structure of RmMan134A-M3 complex
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / Complex
Function / homology: / Glycosyl hydrolase family 134 / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / Uncharacterized protein / Man134A
Function and homology information
Biological speciesRhizopus microsporus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 beta-mannanase.
Authors: You, X. / Qin, Z. / Li, Y.X. / Yan, Q.J. / Li, B. / Jiang, Z.Q.
History
DepositionJun 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_validate_close_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-1,4-mannanase
B: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5834
Polymers36,5742
Non-polymers1,0092
Water5,549308
1
A: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7912
Polymers18,2871
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint16 kcal/mol
Surface area7280 Å2
MethodPISA
2
B: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7912
Polymers18,2871
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint15 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.051, 59.085, 122.092
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 beta-1,4-mannanase


Mass: 18286.934 Da / Num. of mol.: 2 / Fragment: UNP residues 20-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus microsporus (fungus) / Gene: BCV71DRAFT_26579, RMCBS344292_04886 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1NDE2, UniProt: A0A2U8ZTY7*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, HEPES Na, 2-Propanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→30.5 Å / Num. obs: 35620 / % possible obs: 97.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
PHENIXdev-2474-000refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2166 --
Rwork0.1872 --
obs-35620 98 %
Refinement stepCycle: LAST / Resolution: 1.75→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 68 308 2886
LS refinement shellHighest resolution: 1.75 Å / Num. reflection obs: 3386

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