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- PDB-5b2f: N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii co... -

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Basic information

Entry
Database: PDB / ID: 5b2f
TitleN,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii complexed with its inhibitor MPG (phosphate-containing condition)
ComponentsPutative uncharacterized protein PH0499
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Deacetylase Carbohydrate Esterase 14 Inhibitor Complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MQG / Diacetylchitobiose deacetylase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakamura, T. / Niiyama, M. / Ida, K. / Uegaki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology24109017 Japan
Japan Society for the Promotion of Science15K01815 Japan
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii
Authors: Nakamura, T. / Yonezawa, Y. / Tsuchiya, Y. / Niiyama, M. / Ida, K. / Oshima, M. / Morita, J. / Uegaki, K.
History
DepositionJan 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein PH0499
B: Putative uncharacterized protein PH0499
C: Putative uncharacterized protein PH0499
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8709
Polymers94,9033
Non-polymers9686
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-96 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.821, 77.821, 229.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-454-

HOH

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Components

#1: Protein Putative uncharacterized protein PH0499 / N / N'-diacetylchitobiose deacetylase


Mass: 31634.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: PH0499 / Production host: Escherichia coli (E. coli) / References: UniProt: O58235
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-MQG / 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose / ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]-methyl-phosphonamidic acid / 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucose / 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-D-glucose / 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-glucose


Type: D-saccharide, beta linking / Mass: 257.178 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16NO7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 61101 / % possible obs: 94.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data processing
HKL-2000data scaling
BSSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.457 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26988 3087 5.1 %RANDOM
Rwork0.21765 ---
obs0.22033 57838 94.61 %-
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: 35.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 51 186 6787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226849
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9779287
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0885811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25823.743334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.158151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9241545
X-RAY DIFFRACTIONr_chiral_restr0.1440.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1241.54052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78626584
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.02532797
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3244.52703
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: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 204 -
Rwork0.408 4136 -
obs--92.68 %

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