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

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Basic information

Entry
Database: PDB / ID: 2ygy
TitleStructure of wild type E. coli N-acetylneuraminic acid lyase in space group P21 crystal form II
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE / DIRECTED EVOLUTION / SUBSTRATE SPECIFICITY / PROTEIN ENGINEERING
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: 1.9 Å
AuthorsCampeotto, I. / Nelson, A. / Berry, A. / Phillips, S.E.V. / Pearson, A.R.
CitationJournal: Sci Rep / Year: 2018
Title: Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools.
Authors: Campeotto, I. / Lebedev, A. / Schreurs, A.M.M. / Kroon-Batenburg, L.M.J. / Lowe, E. / Phillips, S.E.V. / Murshudov, G.N. / Pearson, A.R.
History
DepositionApr 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 20, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)134,95610
Polymers134,3374
Non-polymers6186
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-103.2 kcal/mol
Surface area41650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.260, 95.870, 91.380
Angle α, β, γ (deg.)90.00, 115.33, 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 / N-ACETYLNEURAMINIC ACID ...N-ACETYLNEURAMINIC ACID LYASE / N-ACETYLNEURAMINATE PYRUVATE- LYASE / N-ACETYLNEURAMINIC ACID ALDOLASE / NALASE / SIALATE LYASE / SIALIC ACID ALDOLASE / SIALIC ACID LYASE


Mass: 33584.367 Da / Num. of mol.: 4
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) / 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: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O
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

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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: 48.41 % / 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: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→47.94 Å / Num. obs: 102699 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0105refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WNN

2wnn


Resolution: 1.9→82.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.232 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5143 5 %RANDOM
Rwork0.194 ---
obs0.196 97526 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.77 Å2
2---0.66 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→82.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 29 653 9870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229464
X-RAY DIFFRACTIONr_bond_other_d0.0010.026378
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.97612816
X-RAY DIFFRACTIONr_angle_other_deg0.8533.00115592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61451208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96524.667420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.218151649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4011550
X-RAY DIFFRACTIONr_chiral_restr0.0690.21450
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021839
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 376 -
Rwork0.305 7087 -
obs--99.44 %

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