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- PDB-6rb7: Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant -

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Basic information

Entry
Database: PDB / ID: 6rb7
TitleRuminococcus gnavus sialic acid aldolase catalytic lysine mutant
ComponentsPutative N-acetylneuraminate lyase
KeywordsLYASE / Neu5Ac / sialic acid / aldolase / ruminococcus gnavus
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / cytosol
Similarity search - Function
N-acetylneuraminate lyase / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / N-acetylneuraminate lyase
Similarity search - Component
Biological species[Ruminococcus] gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 9, 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)150,03422
Polymers148,4144
Non-polymers1,62018
Water32,8951826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-81 kcal/mol
Surface area40450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.181, 121.390, 86.980
Angle α, β, γ (deg.)90.00, 109.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABEF

#1: Protein
Putative N-acetylneuraminate lyase


Mass: 37103.555 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 1844 molecules

#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1826 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris/BICINE Ph 8.5, 20% ethylene glycol, 100mM MgCl2, 10% PEG 8000

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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: 1.6→68.99 Å / Num. obs: 187871 / % possible obs: 99.9 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.043 / Rrim(I) all: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 9303 / CC1/2: 0.878 / Rpim(I) all: 0.192 / Rrim(I) all: 0.285 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4woq

4woq


Resolution: 1.6→68.99 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1508 -4.9091 %random
Rwork0.1285 ---
obs-178613 99.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→68.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9356 0 104 1826 11286

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