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- PDB-6arh: Crystal structure of Human NAL at a resolution of 1.6 Angstrom -

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Basic information

Entry
Database: PDB / ID: 6arh
TitleCrystal structure of Human NAL at a resolution of 1.6 Angstrom
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / sugar metabolism / sialic acid / tetramer
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / Sialic acid metabolism / N-acetylneuraminate catabolic process / carbohydrate metabolic process / identical protein binding / cytosol
Similarity search - Function
N-acetylneuraminate lyase / 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
ACETATE ION / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPearce, F.G. / Bundela, R. / Keown, J.R.
CitationJournal: To Be Published
Title: Crystal structure of Human NAL at a resolution of 1.6 Angstrom
Authors: Pearce, F.G. / Bundela, R. / Keown, J.R.
History
DepositionAug 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,53912
Polymers149,0664
Non-polymers4728
Water22,8971271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALLS, and AUC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-96 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.988, 106.897, 127.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
N-acetylneuraminate lyase / NALase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / ...NALase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialate-pyruvate lyase / Sialic acid aldolase / Sialic acid lyase


Mass: 37266.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPL, C1orf13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXD5, N-acetylneuraminate lyase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1271 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG3350, 0.2 M sodium acetate, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 1, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→49.27 Å / Num. obs: 173953 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.635.51.29785430.5070.6071.436100
8.76-49.275.80.03712060.9960.0170.04199.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5AFD

5afd


Resolution: 1.6→49.27 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.764 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0793 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 8739 5 %RANDOM
Rwork0.1644 ---
obs0.1656 165097 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.46 Å2 / Biso mean: 23.337 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.31 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.6→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9317 0 32 1271 10620
Biso mean--35.48 35.43 -
Num. residues----1204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199650
X-RAY DIFFRACTIONr_bond_other_d0.0020.029120
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.96813078
X-RAY DIFFRACTIONr_angle_other_deg0.907321200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78251238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02325.413412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9591528
X-RAY DIFFRACTIONr_chiral_restr0.0790.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021906
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 636 -
Rwork0.282 12120 -
all-12756 -
obs--99.97 %

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