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- PDB-4n4q: Crystal Structure of N-acetylneuraminate lyase from Mycoplasma sy... -

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Basic information

Entry
Database: PDB / ID: 4n4q
TitleCrystal Structure of N-acetylneuraminate lyase from Mycoplasma synoviae, crystal form II
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
Acylneuraminate lyase
Similarity search - Component
Biological speciesMycoplasma synoviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.1Sep 20, 2023Group: 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: Acylneuraminate lyase
B: Acylneuraminate lyase
C: Acylneuraminate lyase
D: Acylneuraminate lyase


Theoretical massNumber of molelcules
Total (without water)134,6124
Polymers134,6124
Non-polymers00
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-78 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.225, 142.441, 80.792
Angle α, β, γ (deg.)90.000, 108.270, 90.000
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES, pH 6.0, 50 % MPD, 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
ReflectionResolution: 2→76.718 Å / Num. all: 85882 / Num. obs: 85882 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 27.878 Å2 / Rsym value: 0.113 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.113.30.4991.541164123240.49997.6
2.11-2.243.60.3512.142460118560.35198.9
2.24-2.393.50.2642.839310111370.26499.1
2.39-2.583.40.2163.334871103580.21699
2.58-2.833.60.1664.23415295400.16699.1
2.83-3.173.50.1215.43042087030.12199.5
3.17-3.653.40.0896.72629976610.08999.4
3.65-4.483.50.0747.52282064850.07499.6
4.48-6.333.40.06981715050280.06999.4
6.33-47.483.40.0636.4953727900.06399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.9 Å44.59 Å
Translation2.9 Å44.59 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 4N4P

4n4p


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2827 / WRfactor Rwork: 0.2406 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7701 / SU B: 5.852 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2359 / SU Rfree: 0.2009 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 4294 5 %RANDOM
Rwork0.2392 ---
obs0.2413 81494 98.86 %-
all-85788 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.91 Å2 / Biso mean: 27.5753 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å2-0.93 Å2
2---1.8 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9342 0 0 482 9824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229546
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.96712854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15151164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16424.791407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.838151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0171520
X-RAY DIFFRACTIONr_chiral_restr0.0870.21409
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027028
X-RAY DIFFRACTIONr_mcbond_it0.6591.55805
X-RAY DIFFRACTIONr_mcangle_it1.17929285
X-RAY DIFFRACTIONr_scbond_it1.86133741
X-RAY DIFFRACTIONr_scangle_it2.8284.53569
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 322 -
Rwork0.295 5862 -
all-6184 -
obs--96.91 %

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