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- PDB-6oe2: X-Ray Structure of the C-terminal domain (277-440) of Putative ch... -

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Basic information

Entry
Database: PDB / ID: 6oe2
TitleX-Ray Structure of the C-terminal domain (277-440) of Putative chitobiase from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR324A. Re-refinement of 3GGL with correct metal Mn replacing Zn. New metal confirmed with PIXE analysis of original sample.
ComponentsChitobiase
KeywordsHYDROLASE / NESG / BTR324A / Q8A9F0_BACTN / Bacteroides thetaiotaomicron / BT_0865 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Structural Genomics / PIXE
Function / homology
Function and homology information


[protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / metal ion binding
Similarity search - Function
Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / DUF1735 domain-containing protein / Chitobiase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSnell, E.H. / Garman, E.F. / Lowe, E.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target BtR324A
Authors: Kuzin, A. / Neely, H. / Seetharaman, R. / Lee, D. / Ciccosanti, C. / Foote, E.L. / Janjua, H. / Xiao, R. / Nair, R. / Rost, B. / Acton, T. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9283
Polymers18,7671
Non-polymers1612
Water181
1
A: Chitobiase
hetero molecules

A: Chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8566
Polymers37,5342
Non-polymers3224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2270 Å2
ΔGint-14 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.860, 86.860, 50.992
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chitobiase


Mass: 18766.789 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 280-440)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: nagJ_1, ERS852430_00185, SAMN02910322_00414 / Details (production host): PET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ MAGIC
References: UniProt: A0A173R4M5, UniProt: Q8A9F0*PLUS, protein O-GlcNAcase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.75 M magnesium formate, 0.1 M Bis-Tris, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2009 / Details: MIRRORS
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 4644 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 0
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.484 / Num. unique obs: 0 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F2Z

3f2z


Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 42.275 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23661 414 9 %RANDOM
Rwork0.17368 ---
obs0.17916 4201 99.38 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 87.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 8 1 1252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131274
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171169
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6411725
X-RAY DIFFRACTIONr_angle_other_deg1.2711.582718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0695160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98923.7564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.91156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02260
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_it2.3775.47643
X-RAY DIFFRACTIONr_mcbond_other2.3745.471642
X-RAY DIFFRACTIONr_mcangle_it3.7018.212802
X-RAY DIFFRACTIONr_mcangle_other3.7018.213803
X-RAY DIFFRACTIONr_scbond_it2.4545.758630
X-RAY DIFFRACTIONr_scbond_other2.4535.765631
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.928.534924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 28 -
Rwork0.221 298 -
obs--99.09 %
Refinement TLS params.Method: refined / Origin x: -30.74 Å / Origin y: -13.65 Å / Origin z: -5.493 Å
111213212223313233
T0.1696 Å2-0.0549 Å2-0.1024 Å2-0.0422 Å20.0041 Å2--0.2959 Å2
L7.8727 °2-1.6198 °24.0712 °2-2.6579 °2-1.7302 °2--6.275 °2
S-0.4087 Å °-0.1205 Å °1.2674 Å °0.404 Å °-0.1988 Å °-0.6814 Å °-0.3331 Å °0.2188 Å °0.6075 Å °

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