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- PDB-2zzr: Crystal structure of unsaturated glucuronyl hydrolase from Strept... -

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Basic information

Entry
Database: PDB / ID: 2zzr
TitleCrystal structure of unsaturated glucuronyl hydrolase from Streptcoccus agalactiae
ComponentsUnsaturated glucuronyl hydrolase
KeywordsHYDROLASE / alpha barrel
Function / homologyGlycosyltransferase - #10 / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha / :
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.75 Å
AuthorsMaruyama, Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan
Authors: Maruyama, Y. / Nakamichi, Y. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionFeb 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Unsaturated glucuronyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0757
Polymers46,5101
Non-polymers5646
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.080, 116.080, 78.125
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
11A-400-

HOH

21A-793-

HOH

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Components

#1: Protein Unsaturated glucuronyl hydrolase


Mass: 46510.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: 18RS21 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3DUP2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 61457 / % possible obs: 100 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.2
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1VD5

1vd5


Resolution: 1.75→38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.899 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20449 3110 5.1 %RANDOM
Rwork0.18191 ---
obs0.18308 58318 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 33 407 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9494688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16824.101178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74715589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1161518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022663
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21816
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22386
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4571.52056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77423220
X-RAY DIFFRACTIONr_scbond_it1.24931648
X-RAY DIFFRACTIONr_scangle_it1.94.51462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.749→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 233 -
Rwork0.246 4253 -
obs--99.47 %

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