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- PDB-3vxd: Crystal structure of unsaturated glucuronyl hydrolase mutant D115... -

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Basic information

Entry
Database: PDB / ID: 3vxd
TitleCrystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae
ComponentsPutative uncharacterized protein gbs1889
KeywordsHYDROLASE / alpha6/alpha6-barrel
Function / homology
Function and homology information


unsaturated chondroitin disaccharide hydrolase / unsaturated chondroitin disaccharide hydrolase activity / chondroitin 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 Å
AuthorsNakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: To be Published
Title: Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae
Authors: Nakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionSep 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative uncharacterized protein gbs1889
B: Putative uncharacterized protein gbs1889
C: Putative uncharacterized protein gbs1889
D: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,13910
Polymers186,5634
Non-polymers5766
Water12,448691
1
A: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7372
Polymers46,6411
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7372
Polymers46,6411
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8333
Polymers46,6411
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8333
Polymers46,6411
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative uncharacterized protein gbs1889
C: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5705
Polymers93,2812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-5 kcal/mol
Surface area25780 Å2
MethodPISA
6
B: Putative uncharacterized protein gbs1889
D: Putative uncharacterized protein gbs1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5705
Polymers93,2812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-6 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.074, 95.914, 110.886
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46640.695 Da / Num. of mol.: 4 / Mutation: D115N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: NEM316 / Gene: gbs1889 / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: Q8E372, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.5M ammonium sulphate, 0.1M Tris-HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: May 22, 2009
RadiationMonochromator: Fixed exit Si(111) double crystal monochromato
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 136222 / Num. obs: 133399 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 38.8
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.336 / Num. unique all: 13014 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZZR

2zzr


Resolution: 2→27.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.588 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21938 5540 5.1 %RANDOM
Rwork0.18306 ---
obs0.18488 103754 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.432 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å2-0.14 Å2
2---0.53 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11801 0 30 691 12522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212625
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.94217187
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25751512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53624.266654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.748152169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3481565
X-RAY DIFFRACTIONr_chiral_restr0.0770.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219855
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_it0.4451.57380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.842211958
X-RAY DIFFRACTIONr_scbond_it1.13635245
X-RAY DIFFRACTIONr_scangle_it1.8474.55229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 381 -
Rwork0.213 7557 -
obs--97.03 %

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