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- PDB-1f6k: CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEM... -

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Basic information

Entry
Database: PDB / ID: 1f6k
TitleCRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II
ComponentsN-ACETYLNEURAMINATE 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
N-acetylneuraminate lyase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 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 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ACETYLNEURAMINATE LYASE
C: N-ACETYLNEURAMINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,97211
Polymers65,1232
Non-polymers8499
Water16,033890
1
A: N-ACETYLNEURAMINATE LYASE
C: N-ACETYLNEURAMINATE LYASE
hetero molecules

A: N-ACETYLNEURAMINATE LYASE
C: N-ACETYLNEURAMINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,94422
Polymers130,2464
Non-polymers1,69718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13240 Å2
ΔGint-212 kcal/mol
Surface area40180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.774, 118.409, 81.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer constructed from chains A and C generated by the two-fold.

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Components

#1: Protein N-ACETYLNEURAMINATE LYASE


Mass: 32561.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: PKKTAC (VTT BIOTECH, FINLAND) / Production host: Escherichia coli (E. coli) / References: UniProt: P44539, N-acetylneuraminate lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
220 mMTris-HCl1drop
390 mM1dropNaCl
425 %(w/v)PEG40001reservoir
50.2 Mammonium sulfate1reservoir
60.1 M1reservoirNaOAc

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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: Nov 11, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 78230 / Num. obs: 76295 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.39 / Num. unique all: 4180 / % possible all: 46.5
Reflection
*PLUS
Num. measured all: 263507
Reflection shell
*PLUS
% possible obs: 46.5 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.6→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3844 -RANDOM
Rwork0.189 ---
all-76521 --
obs-76521 90.4 %-
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 49 890 5457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg0.024
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 72677
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_d0.064

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