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- PDB-1nal: THE THREE-DIMENSIONAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE FROM... -

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Basic information

Entry
Database: PDB / ID: 1nal
TitleTHE THREE-DIMENSIONAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE FROM ESCHERICHIA COLI
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE
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 / Resolution: 2.2 Å
AuthorsIzard, T. / Lawrence, M.C. / Malby, R.L. / Lilley, G.G. / Colman, P.M.
CitationJournal: 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.
History
DepositionFeb 28, 1994Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEETS PRESENTED AS S1, S2, S3 AND S4 ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS S1, S2, S3 AND S4 ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS 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
1: N-ACETYLNEURAMINATE LYASE
2: N-ACETYLNEURAMINATE LYASE
3: N-ACETYLNEURAMINATE LYASE
4: N-ACETYLNEURAMINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0668
Polymers130,6814
Non-polymers3844
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-129 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.800, 122.800, 198.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO 1 273 / 2: CIS PROLINE - PRO 2 273 / 3: CIS PROLINE - PRO 3 273 / 4: CIS PROLINE - PRO 4 273
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.965127, -0.247604, -0.084981), (-0.248518, 0.764582, 0.594688), (-0.082272, 0.595068, -0.799453)-60.0215, -6.3602, -6.298
2given(0.298026, -0.133676, 0.945151), (-0.134528, -0.986145, -0.097055), (0.94503, -0.098224, -0.31188)3.1421, -164.7988, -27.9705
3given(-0.32847, 0.393964, -0.858429), (0.400407, -0.765066, -0.504329), (-0.855442, -0.509378, 0.093555)-19.02692, -148.59012, -83.41649
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 1 4 .. 1 294 2 4 .. 2 294 0.284 M2 1 4 .. 1 294 3 4 .. 3 294 0.429 M3 1 4 .. 1 294 4 4 .. 4 294 0.702

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Components

#1: Protein
N-ACETYLNEURAMINATE LYASE


Mass: 32670.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6L4, N-acetylneuraminate lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
175 mMsodium phosphate1reservoir
375 mMsodium phosphate1drop
517 mg/mlprotein1drop
60.1 Msodium chloride1drop
70.02 %sodium azide1drop
825 mMTris-HCl1drop
2ammonium sulfate1reservoirsaturated
4ammonium sulfate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 78145 / Num. measured all: 205465 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 55 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.208 -
obs0.208 78144
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8992 0 20 60 9072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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