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- PDB-1f73: CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEM... -

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Basic information

Entry
Database: PDB / ID: 1f73
TitleCRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM III IN COMPLEX WITH SIALIC ACID ALDITOL
ComponentsN-ACETYL NEURAMINATE LYASE
KeywordsLYASE / BETA BARREL
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / 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
Chem-HMN / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsBarbosa, J.A.R.G. / Smith, B.J. / DeGori, R. / Lawrence, M.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme.
Authors: Barbosa, J.A.R.G. / Smith, B.J. / DeGori, R. / Ooi, H.C. / Marcuccio, S.M. / Campi, E.M. / Jackson, W.R. / Brossmer, R. / Sommer, M. / Lawrence, M.C.
History
DepositionJun 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-ACETYL NEURAMINATE LYASE
B: N-ACETYL NEURAMINATE LYASE
C: N-ACETYL NEURAMINATE LYASE
D: N-ACETYL NEURAMINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5849
Polymers130,2464
Non-polymers1,3375
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-46 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.549, 116.727, 129.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer from chains A, B, C, and D.

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Components

#1: Protein
N-ACETYL NEURAMINATE LYASE / NAL


Mass: 32561.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: PKKTAC / Production host: Escherichia coli (E. coli) / References: UniProt: P44539, N-acetylneuraminate lyase
#2: Chemical
ChemComp-HMN / 2,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDO NONANOIC ACID


Mass: 311.286 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H21NO9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
220 mMTris-HCl1drop
390 mM1dropNaCl
421 %(w/v)PEG40001reservoir
50.1 M1reservoirNaOAc
60.1 M1reservoirNH4OAc

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 29, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 90602 / Num. obs: 87977 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Num. unique all: 4473 / % possible all: 97
Reflection
*PLUS
Num. measured all: 382183
Reflection shell
*PLUS
% possible obs: 97 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.95→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huner
RfactorNum. reflection% reflectionSelection details
Rfree0.256 8642 -RANDOM
Rwork0.201 ---
all-86608 --
obs-86608 97.1 %-
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9012 0 90 619 9721
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_deg0.031
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 77966
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.068

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