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- PDB-6rd1: Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant ... -

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Basic information

Entry
Database: PDB / ID: 6rd1
TitleRuminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic acid
ComponentsPutative N-acetylneuraminate lyase
KeywordsLYASE / Neu5Ac / sialic acid / aldolase / ruminococcus gnavus
Function / homologyN-acetylneuraminate lyase / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel / carbohydrate metabolic process / lyase activity / Chem-SI3 / N-acetylneuraminate lyase
Function and homology information
Biological species[Ruminococcus] gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsOwen, C.D. / Bell, A. / Juge, N. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011216/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut.
Authors: Bell, A. / Brunt, J. / Crost, E. / Vaux, L. / Nepravishta, R. / Owen, C.D. / Latousakis, D. / Xiao, A. / Li, W. / Chen, X. / Walsh, M.A. / Claesen, J. / Angulo, J. / Thomas, G.H. / Juge, N.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative N-acetylneuraminate lyase
B: Putative N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8264
Polymers74,2072
Non-polymers6192
Water5,044280
1
A: Putative N-acetylneuraminate lyase
B: Putative N-acetylneuraminate lyase
hetero molecules

A: Putative N-acetylneuraminate lyase
B: Putative N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6518
Polymers148,4144
Non-polymers1,2374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area10370 Å2
ΔGint-58 kcal/mol
Surface area40140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.050, 121.740, 74.470
Angle α, β, γ (deg.)90.000, 119.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative N-acetylneuraminate lyase /


Mass: 37103.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Ruminococcus] gnavus ATCC 29149 (bacteria)
Gene: RUMGNA_02692 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B555
#2: Sugar ChemComp-SI3 / 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid / N-acetylneuraminic acid, ketone form / N-Acetylneuraminic acid


Type: D-saccharide / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris/Bicine pH 8.5, 20% ethylene glycol, 10% PEG 8000, soaked with 5mM Neu5Ac prior to plunge freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.892→68.431 Å / Num. obs: 31874 / % possible obs: 54.3 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.051 / Rrim(I) all: 0.128 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.892-2.1456.21.0061.815950.6560.4291.0958.7
6.257-68.4315.90.03930.715940.9980.0180.04395.9

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
BUSTERrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RAB

6rab


Resolution: 1.892→68.43 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.28 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1566 4.91 %RANDOM
Rwork0.188 ---
obs0.19 30310 53.5 %-
Displacement parametersBiso max: 125.73 Å2 / Biso mean: 37.47 Å2 / Biso min: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.2454 Å20 Å20.2884 Å2
2--2.5624 Å20 Å2
3----2.8079 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.892→68.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 42 280 4984
Biso mean--46.34 39.14 -
Num. residues----608
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1680SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes816HARMONIC5
X-RAY DIFFRACTIONt_it4788HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion636SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5983SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4788HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6472HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion17.99
LS refinement shellResolution: 1.88→2.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2572 28 4.39 %
Rwork0.2103 610 -
all0.2123 638 -
obs--4.92 %

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