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- PDB-4n4p: Crystal Structure of N-acetylneuraminate lyase from Mycoplasma sy... -

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Basic information

Entry
Database: PDB / ID: 4n4p
TitleCrystal Structure of N-acetylneuraminate lyase from Mycoplasma synoviae, crystal form I
ComponentsAcylneuraminate lyase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / cytosol
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 speciesMycoplasma synoviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGeorgescauld, F. / Popova, K. / Gupta, A.J. / Bracher, A. / Engen, J.R. / Hayer-Hartl, M. / Hartl, F.U.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding.
Authors: Georgescauld, F. / Popova, K. / Gupta, A.J. / Bracher, A. / Engen, J.R. / Hayer-Hartl, M. / Hartl, F.U.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylneuraminate lyase
B: Acylneuraminate lyase
C: Acylneuraminate lyase
D: Acylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,89512
Polymers134,6124
Non-polymers2848
Water19,7801098
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-171 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.986, 136.350, 157.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acylneuraminate lyase


Mass: 33652.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma synoviae (bacteria) / Strain: 53 / Gene: MS53_0198, nanA / Plasmid: pET22a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4A6K4, N-acetylneuraminate lyase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES, pH 6.0, 4 % MPD, 0.2 M NaCl, 35 % PEG 400, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.89997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89997 Å / Relative weight: 1
ReflectionRedundancy: 12.9 % / Av σ(I) over netI: 3.6 / Number: 1527148 / Rsym value: 0.176 / D res high: 1.803 Å / D res low: 103.016 Å / Num. obs: 118560 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.748.9299.810.0670.06712.4
4.035.710010.0870.08712.3
3.294.0310010.1070.10712.7
2.853.2910010.1440.14412.8
2.552.8510010.1890.18913.2
2.332.5510010.2320.23212.8
2.162.3310010.2820.28213.5
2.022.1610010.3690.36912.8
1.92.0210010.4920.49213.4
1.81.993.910.6330.63312.2
ReflectionResolution: 1.8→30 Å / Num. all: 113552 / Num. obs: 112371 / % possible obs: 98.96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.808 Å2
Reflection shellResolution: 1.8→1.85 Å / % possible all: 87.52

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å48.93 Å
Translation2.9 Å48.93 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F5Z

1f5z


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1961 / WRfactor Rwork: 0.1643 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.887 / SU B: 2.273 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1218 / SU Rfree: 0.1157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 5913 5 %RANDOM
Rwork0.1729 ---
obs0.1746 112370 98.96 %-
all-112370 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.46 Å2 / Biso mean: 15.5743 Å2 / Biso min: 4.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9264 0 8 1098 10370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229479
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.96512765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60251151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46224.78410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.648151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1921520
X-RAY DIFFRACTIONr_chiral_restr0.090.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026992
X-RAY DIFFRACTIONr_mcbond_it0.7721.55739
X-RAY DIFFRACTIONr_mcangle_it1.45129194
X-RAY DIFFRACTIONr_scbond_it2.50133740
X-RAY DIFFRACTIONr_scangle_it4.224.53571
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 407 -
Rwork0.273 7239 -
all-7646 -
obs--87.52 %

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