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- PDB-5z19: The crystal structure of Ruminococcus gnavus beta-glucuronidase i... -

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Basic information

Entry
Database: PDB / ID: 5z19
TitleThe crystal structure of Ruminococcus gnavus beta-glucuronidase in complex with uronic isofagomine
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
Chem-SJ5 / Beta-glucuronidase
Similarity search - Component
Biological species[Ruminococcus] gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 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 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,58012
Polymers436,6136
Non-polymers9676
Water6,810378
1
A: Beta-glucuronidase
C: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8604
Polymers145,5382
Non-polymers3222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-20 kcal/mol
Surface area42010 Å2
MethodPISA
2
D: Beta-glucuronidase
E: Beta-glucuronidase
F: Beta-glucuronidase
hetero molecules

B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,7208
Polymers291,0754
Non-polymers6454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area15480 Å2
ΔGint-88 kcal/mol
Surface area75170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.282, 112.359, 209.795
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
2LEULEUchain BBB2 - 60226 - 626
3GLUGLUchain CCC2 - 60126 - 625
4GLUGLUchain DDD2 - 59726 - 621
5LYSLYSchain EEE2 - 59826 - 622
6GLUGLUchain FFF2 - 60126 - 625

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Components

#1: Protein
Beta-glucuronidase /


Mass: 72768.805 Da / Num. of mol.: 6 / Fragment: UNP residues 2-603 / Mutation: D290Q, G373A
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: Chemical
ChemComp-SJ5 / (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid


Mass: 161.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H11NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
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: 2.5→30 Å / Num. obs: 142552 / % possible obs: 98.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Χ2: 0.999 / Net I/σ(I): 11.1 / Num. measured all: 453760
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.592.60.705139900.5480.5130.8770.99697.3
2.59-2.692.90.602141970.6650.4050.7291.00399.2
2.69-2.823.20.464142780.7910.2980.5541.00599.5
2.82-2.963.30.338143100.8790.2110.41.00199.5
2.96-3.153.40.238142930.9390.1450.28199.6
3.15-3.393.40.157143260.9710.0950.1841.00899.4
3.39-3.733.40.107142950.9860.0660.1260.99199.2
3.73-4.273.30.076142630.9910.0480.090.99498.8
4.27-5.383.20.058142430.9940.0370.069198.3
5.38-303.10.04143570.9980.0260.0480.99597.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.503→29.916 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 7140 5.01 %
Rwork0.1663 135353 -
obs0.1684 142493 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.01 Å2 / Biso mean: 42.0711 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 2.503→29.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29386 0 66 378 29830
Biso mean--38.23 41.08 -
Num. residues----3587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330320
X-RAY DIFFRACTIONf_angle_d0.90941113
X-RAY DIFFRACTIONf_chiral_restr0.0374239
X-RAY DIFFRACTIONf_plane_restr0.0045330
X-RAY DIFFRACTIONf_dihedral_angle_d12.98711057
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A17573X-RAY DIFFRACTION9.822TORSIONAL
12B17573X-RAY DIFFRACTION9.822TORSIONAL
13C17573X-RAY DIFFRACTION9.822TORSIONAL
14D17573X-RAY DIFFRACTION9.822TORSIONAL
15E17573X-RAY DIFFRACTION9.822TORSIONAL
16F17573X-RAY DIFFRACTION9.822TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5035-2.53190.3512080.28163996420488
2.5319-2.56170.32082550.26234395465097
2.5617-2.59290.31422500.25564517476798
2.5929-2.62570.28932400.24994483472399
2.6257-2.66030.28892140.24334549476399
2.6603-2.69670.30932720.23474455472799
2.6967-2.73520.30252470.23974577482499
2.7352-2.7760.29482450.23284511475699
2.776-2.81930.28772530.230645104763100
2.8193-2.86550.27072440.21374529477399
2.8655-2.91490.25372460.22054501474799
2.9149-2.96780.2742440.21094590483499
2.9678-3.02490.26962330.2134505473899
3.0249-3.08650.28762340.207345674801100
3.0865-3.15360.25922300.197945394769100
3.1536-3.22690.23182400.19454564480499
3.2269-3.30750.21582430.176145664809100
3.3075-3.39680.23072430.17564509475299
3.3968-3.49660.19172350.16344546478199
3.4966-3.60930.18172220.15424556477899
3.6093-3.7380.17562310.14864553478499
3.738-3.88740.19642510.14644519477099
3.8874-4.06390.18032080.13764555476399
4.0639-4.27760.16992580.13144509476798
4.2776-4.54470.16732130.12564539475298
4.5447-4.89420.15472370.11774517475498
4.8942-5.38420.1582130.12544549476298
5.3842-6.15740.17252480.13784518476698
6.1574-7.73540.19182180.15244595481399
7.7354-29.91840.1652650.14474534479996
Refinement TLS params.Method: refined / Origin x: -387.4725 Å / Origin y: -91.2307 Å / Origin z: 887.3725 Å
111213212223313233
T0.2323 Å2-0.0085 Å20.0029 Å2-0.2401 Å20.0067 Å2--0.2432 Å2
L0.0116 °20.0123 °20.0226 °2-0.0282 °20.0099 °2--0.0263 °2
S0.0009 Å °0.0072 Å °-0.0023 Å °0.0129 Å °-0.0031 Å °-0.0098 Å °-0.0064 Å °0.0089 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 597
2X-RAY DIFFRACTION1allB2 - 602
3X-RAY DIFFRACTION1allC2 - 601
4X-RAY DIFFRACTION1allD2 - 597
5X-RAY DIFFRACTION1allE2 - 598
6X-RAY DIFFRACTION1allF2 - 601
7X-RAY DIFFRACTION1allG1 - 6
8X-RAY DIFFRACTION1allS1 - 943

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