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- PDB-1fdy: N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE -

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Basic information

Entry
Database: PDB / ID: 1fdy
TitleN-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE / ALDOLASE / OXO-ACID LYASE / ALPHA-KETO-ACID LYASE / CARBON-CARBON LYASE
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
3-HYDROXYPYRUVIC ACID / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLawrence, M.C. / Barbosa, J.A.R.G. / Smith, B.J. / Hall, N.E. / Pilling, P.A. / Ooi, H.C. / Marcuccio, S.M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase.
Authors: Lawrence, M.C. / Barbosa, J.A.R.G. / Smith, B.J. / Hall, N.E. / Pilling, P.A. / Ooi, H.C. / Marcuccio, S.M.
#1: Journal: Structure / Year: 1994
Title: The Three-Dimensional Structure of N-Acetylneuraminate Lyase from Escherichia Coli
Authors: Izard, T. / Lawrence, M.C. / Malby, R.L. / Lilley, G.G. / Colman, P.M.
#2: Journal: Protein Expr.Purif. / Year: 1992
Title: High-Level Production and Purification of Escherichia Coli N-Acetylneuraminic Acid Aldolase (Ec 4.1.3.3)
Authors: Lilley, G.G. / Von Itzstein, M. / Ivanecic, N.
History
DepositionJul 8, 1996Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Other / Category: citation_author / pdbx_database_status
Item: _citation_author.name / _pdbx_database_status.process_site
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)130,9228
Polymers130,5064
Non-polymers4164
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-41 kcal/mol
Surface area39570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.000, 121.000, 196.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
N-ACETYLNEURAMINATE LYASE / N-ACETYLNEURAMINIC ACID ALDOLASE


Mass: 32626.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COVALENT COMPLEX / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TG1
Description: DESCRIBED IN LILLEY, G.G. ET AL. (1992) SEE REFERENCE 2 BELOW
Gene: NPL / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L4, N-acetylneuraminate lyase
#2: Chemical
ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.9
Details: HANGING DROP VAPOR DIFFUSION. WELL: 53% SATURATED AMMONIUM SULFATE, 75 MILLIMOLAR SODIUM PHOSPHATE BUFFER (PH 6.9). DROP: EQUAL VOLUMES OF WELL SOLUTION AND PRE-REACTED ...Details: HANGING DROP VAPOR DIFFUSION. WELL: 53% SATURATED AMMONIUM SULFATE, 75 MILLIMOLAR SODIUM PHOSPHATE BUFFER (PH 6.9). DROP: EQUAL VOLUMES OF WELL SOLUTION AND PRE-REACTED ENZYME/HYDROXYPYRUVATE COMPLEX (SEE JRNL REFERENCE), vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
153 %(v/v)satammonium salfate1reservoir
275 mMsodium phosphate1reservoir
36.9 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MSC MIRROR SYSTEM
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→100 Å / Num. obs: 60890 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.43 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.6
Reflection shellResolution: 2.44→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.15 / % possible all: 80
Reflection
*PLUS
Num. measured all: 148263
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAL

1nal


Resolution: 2.45→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.219 --
obs0.219 53525 93.2 %
Displacement parametersBiso mean: 32.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8995 0 24 172 9191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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