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- PDB-2wnq: Structure of the E192N mutant of E. coli N-acetylneuraminic acid ... -

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Basic information

Entry
Database: PDB / ID: 2wnq
TitleStructure of the E192N mutant of E. coli N-acetylneuraminic acid lyase in space group P21
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE / SUBSTRATE SPECIFICITY / CARBOHYDRATE METABOLISM / DIRECTED EVOLUTION / PROTEIN ENGINEERING / ALDOLASE
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: 1.8 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 17, 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 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: N-ACETYLNEURAMINATE LYASE
B: N-ACETYLNEURAMINATE LYASE
C: N-ACETYLNEURAMINATE LYASE
D: N-ACETYLNEURAMINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4198
Polymers134,2774
Non-polymers1424
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-102.2 kcal/mol
Surface area41400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 142.770, 84.487
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33569.355 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-297 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKNANA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6L4, N-acetylneuraminate lyase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN D, GLU 192 TO ASN
Sequence detailsALTERNATE LOCI RESULTS IN FOLLOWING DIFFERENCES, T84 IN P0A6L4 IS S84 HERE, G70 IN P0A6L4 IS A70 ...ALTERNATE LOCI RESULTS IN FOLLOWING DIFFERENCES, T84 IN P0A6L4 IS S84 HERE, G70 IN P0A6L4 IS A70 HERE, Q282 IN P0A6L4 IS L282 HERE.

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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: 2.4 Å3/Da / Density % sol: 48.71 % / Description: NONE
Crystal growpH: 8.2 / Details: 100 MM TRIS-HCL PH 8.2, 200 MM NACL, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: May 18, 2009
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,L10.537
11-H,-K,H+L20.463
ReflectionResolution: 1.8→47.59 Å / Num. obs: 110985 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 26.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / % possible all: 97.2

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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: 1.8→39.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.887 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25312 5446 4.9 %RANDOM
Rwork0.1966 ---
obs0.19928 105488 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.724 Å2
Baniso -1Baniso -2Baniso -3
1-11.89 Å20 Å27.32 Å2
2---1.42 Å20 Å2
3----10.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9170 0 4 316 9490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229362
X-RAY DIFFRACTIONr_bond_other_d0.0010.026270
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.97112682
X-RAY DIFFRACTIONr_angle_other_deg0.927315375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27951190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5724.758414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.082151626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8031547
X-RAY DIFFRACTIONr_chiral_restr0.0750.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021812
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_it0.5811.55881
X-RAY DIFFRACTIONr_mcbond_other0.1441.52434
X-RAY DIFFRACTIONr_mcangle_it0.9829442
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.45233481
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1264.53237
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: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 395 -
Rwork0.261 6946 -
obs--87.63 %

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