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- PDB-4ahp: Crystal Structure of Wild Type N-acetylneuraminic acid lyase from... -

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Basic information

Entry
Database: PDB / ID: 4ahp
TitleCrystal Structure of Wild Type N-acetylneuraminic acid lyase from Staphylococcus aureus
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE
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, 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 speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTimms, N. / Polyakova, A. / Windle, C.L. / Trinh, C.H. / Nelson, A. / Trinh, A.R. / Berry, A.
CitationJournal: Chembiochem / Year: 2013
Title: Structural Insights Into the Recovery of Aldolase Activity in N-Acetylneuraminic Acid Lyase by Replacement of the Catalytically Active Lysine with Gamma-Thialysine by Using a Chemical Mutagenesis Strategy.
Authors: Timms, N. / Windle, C.L. / Polyakova, A. / Ault, J.R. / Trinh, C.H. / Pearson, A.R. / Nelson, A. / Berry, A.
History
DepositionFeb 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)135,2388
Polymers135,0974
Non-polymers1424
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-90.4 kcal/mol
Surface area40750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.530, 109.560, 131.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, -0.00731, 0.001651), (-0.007127, 0.9957, 0.09213), (-0.002317, 0.09212, -0.9957)6.972, -3.255, 65.44
2given(-0.947, 0.006007, -0.3212), (0.02409, -0.9957, -0.08965), (-0.3203, -0.09264, 0.9428)17.28, 33.85, 4.582
3given(0.9492, -0.004855, 0.3147), (-0.005317, -1, 0.000609), (0.3147, -0.002251, -0.9492)-10.37, 31.2, 64.22

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Components

#1: Protein
N-ACETYLNEURAMINATE LYASE / N-ACETYLNEURAMINIC ACID LYASE / N-ACETYLNEURAMINATE PYRUVATE-LYASE / N-ACETYLNEURAMINIC ACID ...N-ACETYLNEURAMINIC ACID LYASE / N-ACETYLNEURAMINATE PYRUVATE-LYASE / N-ACETYLNEURAMINIC ACID ALDOLASE / SIALATE LYASE / SIALIC ACID ALDOLASE / SIALIC ACID LYASE


Mass: 33774.145 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q2G160, N-acetylneuraminate lyase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7.4 / Details: 200MM NACL, 100MM TRIS HCL PH 7.4, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→46.52 Å / Num. obs: 68405 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F74

1f74


Resolution: 2.1→46.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.392 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24765 3450 5 %RANDOM
Rwork0.19604 ---
obs0.19868 68405 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9015 0 4 381 9400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.029186
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.96112427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28551136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66825.022456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.138151565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7531542
X-RAY DIFFRACTIONr_chiral_restr0.0990.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217032
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 239 -
Rwork0.218 4245 -
obs--91.4 %

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