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- PDB-1f5z: CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEM... -

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Basic information

Entry
Database: PDB / ID: 1f5z
TitleCRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM I
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: 1.88 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 18, 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: 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)130,2464
Polymers130,2464
Non-polymers00
Water14,088782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-56 kcal/mol
Surface area40120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.753, 109.778, 133.227
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-ACETYLNEURAMINATE LYASE /


Mass: 32561.570 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris-HCl, PEG 4000, NaOAc, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein11
220 mMTris-HCl11
390 mM11NaCl
430 %(w/v)PEG400011precipitant
50.1 MTris-HCl11precipitant
60.1 M11NaOAcprecipitant

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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: Sep 11, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. all: 101661 / Num. obs: 75195 / % possible obs: 74 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.4 / Num. unique all: 4989 / % possible all: 45
Reflection
*PLUS
Num. measured all: 208047
Reflection shell
*PLUS
% possible obs: 45 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.88→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2001 -RANDOM
Rwork0.198 ---
all-74517 --
obs-74517 74 %-
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9164 0 0 782 9946
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_deg0.031
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 72516
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_d0.067

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