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- PDB-6h4e: Proteus mirabilis N-acetylneuraminate lyase -

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Basic information

Entry
Database: PDB / ID: 6h4e
TitleProteus mirabilis N-acetylneuraminate lyase
ComponentsPutative N-acetylneuraminate lyase
KeywordsLYASE / sialic acid / N-acetylneuraminate lyase / NAL
Function / homology
Function and homology information


N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / cytoplasm
Similarity search - Function
DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-acetylneuraminate lyase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.561 Å
AuthorsNorth, R.A. / Garcia-Bonete, M.J. / Goyal, P. / Katona, G. / Dobson, R.C.J. / Friemann, R.
Funding support New Zealand, Sweden, 4items
OrganizationGrant numberCountry
Royal Society of New ZealandUOC1506 New Zealand
Swedish Research Council2011-5790 Sweden
Swedish Research Council2010-1759 Sweden
European Molecular Biology Organization584-2014 New Zealand
CitationJournal: To Be Published
Title: The structure of Proteus mirabilis N-acetylneuraminate lyase reveals an intermolecular disulphide bond
Authors: North, R.A. / Garcia-Bonete, M.J. / Goyal, P. / Katona, G. / Dobson, R.C.J. / Friemann, R.
History
DepositionJul 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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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)63,5094
Polymers63,3172
Non-polymers1922
Water11,800655
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)127,0178
Polymers126,6334
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10470 Å2
ΔGint-150 kcal/mol
Surface area40200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.777, 81.984, 106.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-727-

HOH

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Components

#1: Protein Putative N-acetylneuraminate lyase


Mass: 31658.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Strain: HI4320 / Gene: PMI2973 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4EZY4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.5 M ammonium sulfate, 1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dehydrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.56→44.76 Å / Num. obs: 100351 / % possible obs: 99.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.162 / Net I/σ(I): 7.8
Reflection shellResolution: 1.56→1.65 Å / Rmerge(I) obs: 0.664 / Rrim(I) all: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nal

1nal


Resolution: 1.561→44.757 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.35
RfactorNum. reflection% reflection
Rfree0.1806 4910 4.9 %
Rwork0.1663 --
obs0.167 100268 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.38 Å2 / Biso mean: 11.4543 Å2 / Biso min: 3.18 Å2
Refinement stepCycle: final / Resolution: 1.561→44.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 10 657 5115
Biso mean--21.31 20.72 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054566
X-RAY DIFFRACTIONf_angle_d0.826196
X-RAY DIFFRACTIONf_chiral_restr0.053698
X-RAY DIFFRACTIONf_plane_restr0.005802
X-RAY DIFFRACTIONf_dihedral_angle_d9.4362720
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 (%)
1.5606-1.57840.2491540.22732957311193
1.5784-1.59690.25481640.21813129329399
1.5969-1.61640.26651810.21183106328798
1.6164-1.63690.20591530.2043114326799
1.6369-1.65840.24731450.20743131327699
1.6584-1.68110.23511630.19623121328498
1.6811-1.70510.21461740.18793138331299
1.7051-1.73060.21251720.17983138331099
1.7306-1.75760.22821530.19063125327898
1.7576-1.78650.2461680.18723156332499
1.7865-1.81730.19331250.17943155328099
1.8173-1.85030.19411300.17193207333799
1.8503-1.88590.18781790.16673140331999
1.8859-1.92440.16781780.15483151332999
1.9244-1.96620.16781820.15393125330799
1.9662-2.0120.18881630.15663190335399
2.012-2.06230.19111700.16023187335799
2.0623-2.11810.1891760.16123131330799
2.1181-2.18040.1721680.1593200336899
2.1804-2.25080.17051480.15173185333399
2.2508-2.33120.17951740.155631973371100
2.3312-2.42450.16751480.15532003348100
2.4245-2.53490.18331440.163632383382100
2.5349-2.66850.19691520.166332403392100
2.6685-2.83570.2081410.167732413382100
2.8357-3.05450.17332230.16731933416100
3.0545-3.36180.14941890.156832323421100
3.3618-3.84810.15411650.147432963461100
3.8481-4.84730.14351700.142332843454100
4.8473-44.77520.15961580.18643451360999

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