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- PDB-5a8g: Crystal structure of the wild-type Staphylococcus aureus N- acety... -

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Basic information

Entry
Database: PDB / ID: 5a8g
TitleCrystal structure of the wild-type Staphylococcus aureus N- acetylneurminic acid lyase in complex with fluoropyruvate
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: 1.72 Å
AuthorsStockwell, J. / Daniels, A.D. / Windle, C.L. / Harman, T. / Woodhall, T. / Trinh, C.H. / Lebel, T. / Pearson, A.R. / Mulholland, K. / Berry, A. / Nelson, A.
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: Evaluation of Fluoropyruvate as Nucleophile in Reactions Catalysed by N-Acetyl Neuraminic Acid Lyase Variants: Scope, Limitations and Stereoselectivity.
Authors: Stockwell, J. / Daniels, A.D. / Windle, C.L. / Harman, T.A. / Woodhall, T. / Lebl, T. / Trinh, C.H. / Mulholland, K. / Pearson, A.R. / Berry, A. / Nelson, A.
History
DepositionJul 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL ... 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. SHEET DETERMINATION METHOD: DSSP 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.

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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


Theoretical massNumber of molelcules
Total (without water)68,2432
Polymers68,2432
Non-polymers00
Water6,233346
1
A: N-ACETYLNEURAMINATE LYASE
B: N-ACETYLNEURAMINATE LYASE

A: N-ACETYLNEURAMINATE LYASE
B: N-ACETYLNEURAMINATE LYASE


Theoretical massNumber of molelcules
Total (without water)136,4864
Polymers136,4864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area10510 Å2
ΔGint-52.5 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.587, 150.396, 140.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8514, 0.004464, -0.5244), (-0.004126, -1, 0.001812), (-0.5244, 0.000621, 0.8514)
Vector: -39.83, 100.3, -11.23)

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Components

#1: Protein N-ACETYLNEURAMINATE LYASE / N-ACETYLNEURAMINIC ACID LYASE / NAL / NEU5AC LYASE / N-ACETYLNEURAMINATE PYRUVATE-LYASE / N- ...N-ACETYLNEURAMINIC ACID LYASE / NAL / NEU5AC LYASE / N-ACETYLNEURAMINATE PYRUVATE-LYASE / N-ACETYLNEURAMINIC ACID ALDOLASE / SIALATE LYASE / SIALIC ACID ALDOLASE / SIALIC ACID LYASE


Mass: 34121.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE BETWEEN K165 AND FLUOROPYRUVATE
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
Description: STANDARD LABORATORY STRAIN / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q2G160, N-acetylneuraminate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details(2S)-2-AMINO-5-[(1-CARBOXY-2-FLUOROETHYL)AMINO]PENTANOIC ACID (KPF): FLUOROPYRUVATE COVALENTLY ...(2S)-2-AMINO-5-[(1-CARBOXY-2-FLUOROETHYL)AMINO]PENTANOIC ACID (KPF): FLUOROPYRUVATE COVALENTLY LINKED TO LYSINE

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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: 49.36 % / Description: NONE
Crystal growDetails: 200MM NACL, 100MM TRIS/HCL PH 7.0-8.5, 18-28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.71→28.89 Å / Num. obs: 70045 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AHP

4ahp


Resolution: 1.72→75.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.569 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21144 3530 5 %RANDOM
Rwork0.18106 ---
obs0.18259 66406 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.804 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.76 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.72→75.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 0 346 4976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194732
X-RAY DIFFRACTIONr_bond_other_d0.0010.024569
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9726407
X-RAY DIFFRACTIONr_angle_other_deg0.8763.00210499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73525.214234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61115821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4181522
X-RAY DIFFRACTIONr_chiral_restr0.1150.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021087
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_it0.9121.3052332
X-RAY DIFFRACTIONr_mcbond_other0.911.3052331
X-RAY DIFFRACTIONr_mcangle_it1.4221.9532913
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6821.5352400
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: 1.717→1.762 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 206 -
Rwork0.222 4170 -
obs--84.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32330.0171-0.01120.4716-0.08091.1013-0.07410.0242-0.0486-0.08230.0151-0.02090.30770.02930.0590.1252-0.01270.0380.0179-0.02170.0526-28.669231.516717.9338
20.4228-0.1925-0.29990.63820.22781.71240.00910.01790.0081-0.1040.018-0.0414-0.31460.0918-0.02710.0925-0.045-0.00550.03810.00680.0424-24.556568.827919.1258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 293
2X-RAY DIFFRACTION2B3 - 293

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