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- PDB-3ani: Crystal structure of unsaturated glucuronyl hydrolase mutant D175... -

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Basic information

Entry
Database: PDB / ID: 3ani
TitleCrystal structure of unsaturated glucuronyl hydrolase mutant D175N from Streptcoccus agalactiae
ComponentsPutative uncharacterized protein gbs1889
KeywordsHYDROLASE / alpha6/alpha6-barrel
Function / homology
Function and homology information


unsaturated chondroitin disaccharide hydrolase / chondroitin hydrolase activity / unsaturated chondroitin disaccharide hydrolase activity / polysaccharide catabolic process
Similarity search - Function
Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Unsaturated chondroitin disaccharide hydrolase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups
Authors: Nakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionSep 2, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein gbs1889


Theoretical massNumber of molelcules
Total (without water)46,6411
Polymers46,6411
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein gbs1889

A: Putative uncharacterized protein gbs1889


Theoretical massNumber of molelcules
Total (without water)93,2812
Polymers93,2812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2160 Å2
ΔGint-9 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.117, 53.372, 70.165
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein gbs1889 / Unsaturated glucuronyl hydrolase


Mass: 46640.691 Da / Num. of mol.: 1 / Mutation: D175N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: serogroup III/NEM316 / Gene: gbs1889, Ugl / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174
References: UniProt: Q8E372, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 41.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% ethylene glycol, 5% PEG 3000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2009
RadiationMonochromator: Fixed exit Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 13575 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.352 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZZR

2zzr


Resolution: 2.5→29.16 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.38 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26002 657 4.9 %RANDOM
Rwork0.18709 ---
obs0.19039 12769 98.9 %-
all-12911 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.806 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å21.45 Å2
2--0.21 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 0 61 3188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223313
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.9434505
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2445395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87924.277173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26115567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9171517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212593
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_it0.4451.51939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82423138
X-RAY DIFFRACTIONr_scbond_it0.87131374
X-RAY DIFFRACTIONr_scangle_it1.4564.51367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 53 -
Rwork0.215 925 -
obs-925 98.09 %

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