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- PDB-5z18: The crystal structure of Ruminococcus gnavus beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 5z18
TitleThe crystal structure of Ruminococcus gnavus beta-glucuronidase
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / beta-glucuronidase / GH2
Function / homology
Function and homology information


beta-glucuronidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily ...Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsDashnyam, P. / Lin, H.Y. / Lin, C.H.
CitationJournal: To Be Published
Title: Dissection of the substrate preference and structure of gut microbial beta-glucuronidases identifies the major bacteria causing xenobiotic toxicity
Authors: Dashnyam, P. / Mudududdla, R. / Hsieh, T.J. / Lin, T.C. / Lin, H.Y. / Chen, P.Y. / Hsu, C.Y. / Lin, C.H.
History
DepositionDec 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase
C: Beta-glucuronidase
D: Beta-glucuronidase
E: Beta-glucuronidase
F: Beta-glucuronidase


Theoretical massNumber of molelcules
Total (without water)436,6136
Polymers436,6136
Non-polymers00
Water27,7611541
1
A: Beta-glucuronidase
B: Beta-glucuronidase


Theoretical massNumber of molelcules
Total (without water)145,5382
Polymers145,5382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-22 kcal/mol
Surface area42410 Å2
MethodPISA
2
C: Beta-glucuronidase
E: Beta-glucuronidase
F: Beta-glucuronidase

D: Beta-glucuronidase


Theoretical massNumber of molelcules
Total (without water)291,0754
Polymers291,0754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area15340 Å2
ΔGint-88 kcal/mol
Surface area76140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.868, 118.182, 210.355
Angle α, β, γ (deg.)90.000, 93.450, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUchain AAA2 - 59726 - 621
2GLUGLUchain BBB2 - 59726 - 621
3LYSLYSchain CCC2 - 59926 - 623
4PHEPHEchain DDD2 - 60326 - 627
5LYSLYSchain EEE2 - 59926 - 623
6GLUGLUchain FFF2 - 59726 - 621

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Components

#1: Protein
Beta-glucuronidase /


Mass: 72768.805 Da / Num. of mol.: 6 / Fragment: UNP residues 2-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: uidA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6W7J7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1541 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium Citrate buffer, pH 4.3, 100mM Sodium Citrate salt, 22%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.495→30 Å / Num. obs: 151886 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.055 / Rrim(I) all: 0.109 / Χ2: 1.001 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.90.41151970.8660.2350.4741.00599.2
2.59-2.6940.324152690.920.1830.3731.00899.8
2.69-2.8240.255152520.9420.1440.2941.00499.8
2.82-2.9640.193152940.9660.1080.2220.99599.8
2.96-3.1540.148152880.9780.0840.1710.99999.8
3.15-3.393.90.108153310.9880.0620.1251.00599.5
3.39-3.733.80.086152060.9910.050.10.99899.1
3.73-4.273.50.065149630.9940.040.0760.99497.5
4.27-5.383.30.055148580.9940.0360.0661.00496
5.38-303.30.052152280.9950.0340.0620.99797.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.495→29.033 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2094 1921 1.32 %
Rwork0.1672 --
obs0.1678 145628 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.79 Å2 / Biso mean: 36.5238 Å2 / Biso min: 14.53 Å2
Refinement stepCycle: final / Resolution: 2.495→29.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28892 0 0 1541 30433
Biso mean---38.2 -
Num. residues----3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929718
X-RAY DIFFRACTIONf_angle_d1.23840288
X-RAY DIFFRACTIONf_chiral_restr0.0514146
X-RAY DIFFRACTIONf_plane_restr0.0065217
X-RAY DIFFRACTIONf_dihedral_angle_d13.27710829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A17314X-RAY DIFFRACTION8.58TORSIONAL
12B17314X-RAY DIFFRACTION8.58TORSIONAL
13C17314X-RAY DIFFRACTION8.58TORSIONAL
14D17314X-RAY DIFFRACTION8.58TORSIONAL
15E17314X-RAY DIFFRACTION8.58TORSIONAL
16F17314X-RAY DIFFRACTION8.58TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4954-2.55770.28831170.22799078919584
2.5577-2.62690.24531350.22739837997291
2.6269-2.70410.34091280.219999581008692
2.7041-2.79130.27931380.2152101391027793
2.7913-2.8910.24511360.2096102451038194
2.891-3.00660.25781340.199103571049195
3.0066-3.14330.23121400.1903103781051896
3.1433-3.30880.21351510.1732104921064396
3.3088-3.51580.20921400.163105031064397
3.5158-3.78670.20861370.1571105581069597
3.7867-4.16680.1671450.14104851063096
4.1668-4.76740.17931330.1337103651049895
4.7674-5.99780.16941420.1448105381068096
5.9978-29.03480.18621450.1553107741091997
Refinement TLS params.Method: refined / Origin x: -388.6749 Å / Origin y: -76.6505 Å / Origin z: 890.0285 Å
111213212223313233
T0.2538 Å20.0132 Å20.0036 Å2-0.2188 Å2-0.005 Å2--0.2267 Å2
L0.0459 °20.0274 °20.0025 °2-0.0372 °20.0039 °2--0.0343 °2
S-0.0043 Å °-0.0053 Å °-0.0107 Å °-0.0055 Å °-0.0003 Å °-0.0111 Å °0.0039 Å °-0.0006 Å °0.0047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 597
2X-RAY DIFFRACTION1allB2 - 597
3X-RAY DIFFRACTION1allC2 - 599
4X-RAY DIFFRACTION1allD2 - 603
5X-RAY DIFFRACTION1allE2 - 599
6X-RAY DIFFRACTION1allF2 - 597
7X-RAY DIFFRACTION1allA701 - 965
8X-RAY DIFFRACTION1allB701 - 940
9X-RAY DIFFRACTION1allC701 - 968
10X-RAY DIFFRACTION1allD701 - 924
11X-RAY DIFFRACTION1allE701 - 950
12X-RAY DIFFRACTION1allF701 - 994

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