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- PDB-4aho: Crystal Structure of N-acetylneuraminic acid lyase from Staphyloc... -

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Basic information

Entry
Database: PDB / ID: 4aho
TitleCrystal Structure of N-acetylneuraminic acid lyase from Staphylococcus aureus with the chemical modification thia-lysine at position 165
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 / OTHER / Resolution: 2 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 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)135,8318
Polymers135,6894
Non-polymers1424
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-90.6 kcal/mol
Surface area40090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.315, 109.719, 131.373
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(-0.9999, -0.01052, 0.002089), (-0.01027, 0.9955, 0.09469), (-0.003076, 0.09466, -0.9955)7.137, -3.242, 65.4
2given(-0.9497, 0.01067, -0.3131), (0.01951, -0.9955, -0.09311), (-0.3126, -0.09454, 0.9452)17.06, 33.94, 4.539
3given(0.9517, -0.001391, 0.307), (-0.001579, -1, 0.000364), (0.307, -0.000831, -0.9517)-10.19, 31.1, 64.28

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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: 33922.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CHEMICAL MODIFICATION THIA-LYSINE AT POSITION 165. MISSING LOOP 138-146 CHAIN A, B, C, D
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.: 362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: Oct 6, 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→29.43 Å / Num. obs: 80641 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 1.95→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→29.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.47 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23534 4032 5 %RANDOM
Rwork0.19572 ---
obs0.19773 80641 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.057 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--1.57 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8923 0 4 362 9289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.029087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.96512290
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28851123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97725.122451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8261542
X-RAY DIFFRACTIONr_chiral_restr0.1080.21369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216946
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 267 -
Rwork0.246 5270 -
obs--99.98 %
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)
10.568-0.03340.27811.2797-0.17410.9155-0.0413-0.066-0.03710.36970.08920.2424-0.1669-0.1463-0.04790.49840.05710.10650.03030.01470.1533-17.9312.48747.514
20.52760.15040.35051.1836-0.05131.0510.05250.1254-0.0240.0059-0.0847-0.25770.020.23080.03220.32170.02540.02770.08560.00220.183824.8914.64119.227
31.0262-0.0555-0.53711.1588-0.27481.29420.1267-0.11430.00230.4239-0.1485-0.2112-0.34690.22770.02180.6619-0.1023-0.14950.05890.00060.152419.29716.66653.495
40.6368-0.0391-0.1171.2449-0.00170.63640.00050.0675-0.0504-0.12090.00410.1277-0.0111-0.0453-0.00460.36990.0395-0.04120.0339-0.00330.1299-12.44518.63613.691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 293
2X-RAY DIFFRACTION2B-1 - 293
3X-RAY DIFFRACTION3C2 - 293
4X-RAY DIFFRACTION4D3 - 293

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