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- PDB-2w3z: Structure of a Streptococcus mutans CE4 esterase -

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Basic information

Entry
Database: PDB / ID: 2w3z
TitleStructure of a Streptococcus mutans CE4 esterase
ComponentsPUTATIVE DEACETYLASE
KeywordsHYDROLASE / PGDA / GLCNAC DE-N-ACETYLASE / DIVALE METAL CATION DEPENDENT / CARBOHYDRATE ESTERASE FAMILY 4 / CELL SURFACE SURFACE DEACETYLASE
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
: / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Deacetylase
Similarity search - Component
Biological speciesSTREPTOCOCCUS MUTANS UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsDeng, D.M. / Urch, J.E. / ten Cate, J.M. / Rao, V.A. / van Aalten, D.M.F. / Crielaard, W.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Streptococcus Mutans Smu.623C Codes for a Functional, Metal Dependent Polysaccharide Deacetylase that Modulates Interactions with Salivary Agglutinin.
Authors: Deng, D.M. / Urch, J.E. / Ten Cate, J.M. / Rao, V.A. / Van Aalten, D.M.F. / Crielaard, W.
History
DepositionNov 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
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

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Assembly

Deposited unit
A: PUTATIVE DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0514
Polymers34,7961
Non-polymers2553
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)128.306, 128.306, 128.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein PUTATIVE DEACETYLASE / POLYSACCHARIDE DEACETYLASE


Mass: 34796.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZINC AND PHOSPHATE IN ACTIVE SITE, N-TERMINAL SIGNAL PEPTIDE REMOVED
Source: (gene. exp.) STREPTOCOCCUS MUTANS UA159 (bacteria) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q8DV82, chitin deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.9 Å3/Da / Density % sol: 57.1 % / Description: NONE
Crystal growpH: 5.6 / Details: 2.4 M NA/K PHOSPHATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.45→15 Å / Num. obs: 61316 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.9
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.6 / % possible all: 98.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
WARPNTRACEphasing
CNSrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.45→15 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.1853 1251 2 %
Rwork0.1647 --
obs0.1647 61312 99 %
Solvent computationBsol: 50.7675 Å2 / ksol: 0.382994 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 11 299 2171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01239
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.70734
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.45→1.5 Å / Num. reflection Rwork: 6070 / Total num. of bins used: 10
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: ION.TOP

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