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- PDB-3lbc: D-sialic acid aldolase complexed with L-arabinose -

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Basic information

Entry
Database: PDB / ID: 3lbc
TitleD-sialic acid aldolase complexed with L-arabinose
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / Tim barrel / Carbohydrate metabolism / Schiff base
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
L-arabinose / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChou, C.-Y. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: To be Published
Title: Modulation of substrate specificities of D-sialic acid aldolase through single mutations of Val251
Authors: Chou, C.-Y. / Ko, T.-P. / Wu, K.-J. / Huang, K.-F. / Lin, C.-H. / Wong, C.-H. / Wang, A.H.-J.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 1, 2020Group: Advisory / Atomic model / Database references
Category: atom_site / pdbx_validate_close_contact / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_ref_seq_dif.details
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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-acetylneuraminate lyase
B: N-acetylneuraminate lyase
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,53416
Polymers141,1654
Non-polymers1,36912
Water22,5191250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-57 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.174, 121.174, 199.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 35291.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3225, JW3194, nanA, npl / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6L4, N-acetylneuraminate lyase
#2: Sugar
ChemComp-LAI / L-arabinose


Type: L-saccharide / Mass: 150.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1250 / 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 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M ammonium sulfate, 0.1M Bis-Tris,pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 26, 2008 / Details: vertically focusing mirror
RadiationMonochromator: horizontally focusing single crystal Si(111) bent Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 144750 / Num. obs: 143303 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 35.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.8 / Num. unique all: 14319 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 1NAL

1nal


Resolution: 1.85→26.24 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 6860 -RANDOM
Rwork0.1878 ---
all0.18897 135539 --
obs0.18897 128679 89 %-
Solvent computationBsol: 65.534 Å2
Displacement parametersBiso mean: 32.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.295 Å2-0.49 Å20 Å2
2--0.295 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→26.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9107 0 80 1250 10437
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.31055
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_mcbond_it1.1611.5
X-RAY DIFFRACTIONc_scbond_it1.9922
X-RAY DIFFRACTIONc_mcangle_it1.7472
X-RAY DIFFRACTIONc_scangle_it2.9892.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.0201
RfactorNum. reflection% reflection
Rfree0.2967 639 -
Rwork0.2766 --
obs-12081 84.37 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ara.par
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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