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- PDB-2wo5: Structure of wild type E. coli N-acetylneuraminic acid lyase in s... -

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Basic information

Entry
Database: PDB / ID: 2wo5
TitleStructure of wild type E. coli N-acetylneuraminic acid lyase in space group P21 crystal form I
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE / SUBSTRATE SPECIFICITY / CARBOHYDRATE METABOLISM / DIRECTED EVOLUTION / PROTEIN ENGINEERING / ALDOLASE / SCHIFF BASE
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / single-species biofilm formation / carbohydrate metabolic process / identical protein binding / cytosol
Similarity search - Function
N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / 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 speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCampeotto, I. / Bolt, A.H. / Harman, T.A. / Trinh, C.H. / Dennis, C.A. / Phillips, S.E.V. / Pearson, A.R. / Nelson, A. / Berry, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Insights Into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution.
Authors: Campeotto, I. / Bolt, A.H. / Harman, T.A. / Dennis, C.A. / Trinh, C.H. / Phillips, S.E.V. / Nelson, A. / Pearson, A.R. / Berry, A.
History
DepositionJul 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLNEURAMINATE LYASE
B: N-ACETYLNEURAMINATE LYASE
C: N-ACETYLNEURAMINATE LYASE
D: N-ACETYLNEURAMINATE LYASE


Theoretical massNumber of molelcules
Total (without water)134,3374
Polymers134,3374
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-59.8 kcal/mol
Surface area40910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.795, 142.167, 84.180
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-ACETYLNEURAMINATE LYASE / N-ACETYLNEURAMINIC ACID ALDOLASE / N-ACETYLNEURAMINATE PYRUVATE-LYASE / SIALIC ACID LYASE / SIALATE ...N-ACETYLNEURAMINIC ACID ALDOLASE / N-ACETYLNEURAMINATE PYRUVATE-LYASE / SIALIC ACID LYASE / SIALATE LYASE / SIALIC ACID ALDOLASE / NALASE


Mass: 33584.367 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Plasmid: PKNANA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6L4, N-acetylneuraminate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.38 Å3/Da / Density % sol: 48.85 % / Description: NONE
Crystal growpH: 8 / Details: 100MM TRIS-HCL PH 8.0, 200MM NACL, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.628
11-H,-K,H+L20.372
ReflectionResolution: 2.2→79.56 Å / Num. obs: 61635 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0097refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WNN

2wnn


Resolution: 2.2→71.09 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.361 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27151 3083 5 %RANDOM
Rwork0.21126 ---
obs0.21424 58519 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.076 Å2
Baniso -1Baniso -2Baniso -3
1-25.43 Å20 Å29.56 Å2
2--1.78 Å20 Å2
3----27.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9127 0 0 169 9296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229352
X-RAY DIFFRACTIONr_bond_other_d0.0010.026277
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.97512674
X-RAY DIFFRACTIONr_angle_other_deg0.93315405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9251197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08724.843413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.416151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1251547
X-RAY DIFFRACTIONr_chiral_restr0.0770.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021805
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5991.55874
X-RAY DIFFRACTIONr_mcbond_other0.131.52430
X-RAY DIFFRACTIONr_mcangle_it1.04829437
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.61933478
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.464.53228
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 242 -
Rwork0.259 4132 -
obs--97.5 %

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