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- PDB-2wkj: Crystal structure of the E192N mutant of E. Coli N-acetylneuramin... -

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Basic information

Entry
Database: PDB / ID: 2wkj
TitleCrystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate at 1.45A resolution in space group P212121
ComponentsN-ACETYLNEURAMINATE LYASE
KeywordsLYASE / DIRECTED EVOLUTION / SIALIC ACID MIMETICS / ALDOLASE / SCHIFF BASE / CARBOHYDRATE METABOLISM / N-ACETYLNEURAMINIC ACID LYASE
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
PYRUVIC ACID / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCampeotto, I. / Carr, S.B. / Trinh, C.H. / Nelson, A.S. / Berry, A. / Phillips, S.E.V. / Pearson, A.R.
CitationJournal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2009
Title: Structure of an Escherichia coli N-acetyl-D-neuraminic acid lyase mutant, E192N, in complex with pyruvate at 1.45 angstrom resolution.
Authors: Campeotto, I. / Carr, S.B. / Trinh, C.H. / Nelson, A.S. / Berry, A. / Phillips, S.E. / Pearson, A.R.
History
DepositionJun 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 19, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.2Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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)134,9788
Polymers134,3254
Non-polymers6534
Water23,5461307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-46.36 kcal/mol
Surface area40410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.329, 108.049, 148.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33581.344 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-296 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE BETWEEN K165 AND PYRUVATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PKKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): EP-MAX 10B COMPETENT CELLS / References: UniProt: P0A6L4, N-acetylneuraminate lyase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1307 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLU 192 TO ASN ENGINEERED RESIDUE IN CHAIN D, GLU 192 TO ASN
Nonpolymer detailsPOLYETHYLENE GLYCOL 400 (1PE): PARTIAL PEG400 PRESENT
Sequence detailsN-TERMINAL TAG RESIDUES HHEAT IN ALL CHAINS.P0A6L4 3 RESIDUES DIFFER FROM P0A6L4 AS AN ALTERNATE ...N-TERMINAL TAG RESIDUES HHEAT IN ALL CHAINS.P0A6L4 3 RESIDUES DIFFER FROM P0A6L4 AS AN ALTERNATE LOCI WAS USED FOR THIS CLONE. THESE RESIDUES ARE 84 (THR IN P0A6L4 SER HERE), 70 (GLY IN P0A6L4 ALA HERE) AND 282 (GLN IN P0A6L4 AND LEU HERE)

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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: 2.34 Å3/Da / Density % sol: 47.51 % / Description: NONE
Crystal growpH: 8.2
Details: 100MM TRIS HCL, PH 8.2, 200MM AMMONIUM ACETATE, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 1.45→63.42 Å / Num. obs: 213226 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 14.333 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAL

1nal


Resolution: 1.45→87.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.266 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 0 AND 1 HAVE BEEN MODELLED WITH CB ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18857 10718 5 %RANDOM
Rwork0.16665 ---
obs0.16775 202361 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--1.13 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.45→87.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 28 1307 10523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229553
X-RAY DIFFRACTIONr_bond_other_d00.028830
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.97712960
X-RAY DIFFRACTIONr_angle_other_deg1.268320516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59251235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54824.846423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.148151668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641549
X-RAY DIFFRACTIONr_chiral_restr0.0790.21470
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110718
X-RAY DIFFRACTIONr_gen_planes_other00.021841
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_it0.5921.55971
X-RAY DIFFRACTIONr_mcbond_other0.1991.52477
X-RAY DIFFRACTIONr_mcangle_it0.98429597
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87933582
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8994.53340
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: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 699 -
Rwork0.277 13091 -
obs--84.63 %
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)
122.34768.1919-1.75273.0358-0.64540.13950.6532-2.5146-2.24810.2022-0.8544-0.9489-0.06860.19630.20120.3284-0.105-0.03780.7746-0.00120.739928.041-10.56721.065
22.0519-0.21620.03831.3519-0.32930.8724-0.0533-0.1702-0.13020.11780.04620.08810.0698-0.04060.00710.15110.00150.00360.07440.03690.02524.488-20.05231.537
31.14320.01020.05561.0270.07930.9338-0.0218-0.1717-0.02410.0870.0016-0.0080.06660.05170.02020.12830.0004-0.00030.09020.02830.010110.658-14.77431.182
40.4917-0.0878-0.10340.48710.16790.4715-0.0032-0.05580.04080.01390.0072-0.0363-0.05680.0723-0.0040.1108-0.0112-0.00970.0761-0.00260.006112.876-0.24825.251
50.44340.0077-0.24770.4544-0.0290.51770.0039-0.0467-0.00770.0016-0.0149-0.0277-0.03980.09930.0110.1165-0.018-0.00360.06960.01180.003618.326-8.81911.689
63.9926-1.05121.23842.4239-0.32693.8924-0.08350.2179-0.2659-0.1151-0.0311-0.07320.27480.51190.11460.14210.03940.03410.10380.02440.045319.303-27.1549.502
71.0514-0.0374-0.37080.34470.13821.3914-0.0433-0.0462-0.12390.0247-0.02240.0360.0862-0.05790.06570.1303-0.0160.00670.03360.02980.0479-0.891-22.66320.082
87.642-0.56611.10336.802-1.71723.1351-0.1637-0.0022-0.4852-0.1905-0.0243-0.47050.37240.04460.1880.1613-0.02410.07140.01350.00090.111-0.013-31.99918.148
90.54220.21090.63811.67221.52812.405-0.0040.13240.1689-0.1682-0.047-0.0804-0.3992-0.14080.05090.20110.0505-0.0050.15370.07530.094-13.93717.884-18.386
101.4795-0.2029-0.54313.66630.64691.76240.04220.21990.1172-0.08280.04440.29490.0124-0.264-0.08670.0980.0146-0.02660.20530.06240.0525-21.6085.825-28.022
111.1176-0.27770.10820.4336-0.10990.73330.02440.13640.107-0.05340.0023-0.0234-0.09-0.0514-0.02670.10180.02270.00210.09350.04840.0292-6.58111.764-24.099
122.6257-2.06051.82652.6803-1.74394.29040.00420.17430.3614-0.02480.0007-0.1995-0.26750.222-0.00490.116-0.01140.01880.07960.04790.09045.01818.084-19.883
130.55440.2552-0.21360.62290.0860.74870.01340.06250.14560.00960.01580.0165-0.1234-0.032-0.02920.12050.0239-0.00370.0580.03360.0521-10.08217.687-7.347
141.61120.2544-0.52414.17131.02132.23670.0856-0.00950.30290.0360.00070.2066-0.2307-0.3381-0.08630.09850.05370.01030.13630.02380.0721-26.88713.833-2.581
151.8752-0.5234-0.33780.62250.03430.46470.01490.139-0.08320.0001-0.00450.08280.0605-0.0761-0.01040.0625-0.0107-0.0210.12290.01680.0204-21.489-2.325-18.663
166.2013-2.30490.22123.9402-0.59272.0580.00970.1492-0.00670.065-0.08750.0257-0.0248-0.13070.07780.0461-0.0147-0.01080.13550.02550.034-32.119-0.203-13.376
179.67486.8016-2.39455.5028-1.62560.6138-0.52420.562-0.8357-0.47210.333-0.38530.1977-0.13730.19130.45440.0033-0.07780.1471-0.07530.23089.836-27.539-16.471
180.72270.364-0.36842.6876-0.76261.45670.00720.1357-0.0277-0.04430.0245-0.07680.00390.0602-0.03170.07520.00850.00120.1049-0.00250.006819.283-4.095-26.713
190.9355-0.13980.02691.45720.10181.04450.00010.1514-0.0323-0.04960.018-0.07490.12590.0607-0.01810.09180.01370.0050.0948-0.00780.005814.179-10.462-26.147
200.9152-0.04170.17220.3685-0.2680.5022-0.00440.0974-0.0896-0.02840.03610.04020.1029-0.0654-0.03160.1008-0.0098-0.01180.0726-0.00520.0152-0.366-12.54-20.214
210.67520.1660.11380.4601-0.27380.76290.00510.0303-0.0581-0.03310.00230.01160.12-0.012-0.00740.11920.0001-0.00350.0391-0.00160.007810.976-17.925-7.36
220.8432-0.0796-0.13194.496-1.01191.9413-0.0198-0.0322-0.07990.0331-0.0366-0.16540.12780.27270.05640.09640.0251-0.00230.10090.02020.018226.455-12.613-3.318
231.67060.03890.2970.7332-0.03690.6337-0.00670.0630.12310.0164-0.0247-0.0691-0.04350.02590.03140.08-0.00620.00120.08310.0240.0222.8244.556-17.452
247.1838-0.2114-0.63545.7144-1.66113.9253-0.05420.1314-0.3357-0.0682-0.0323-0.28550.1650.12680.08650.04740.0080.00150.08630.0210.055434.666-4.079-14.415
2510.279.27723.375914.52196.60223.16650.7038-1.9121.47581.1198-2.08272.87640.5314-0.85071.37890.3154-0.15330.1840.9869-0.11430.7118-28.1139.94421.326
261.81740.2144-0.02441.14410.42890.7199-0.1133-0.21880.12970.1520.0575-0.0268-0.1411-0.00510.05580.20890.02-0.01410.0999-0.06190.0454-4.83319.02332.22
271.4893-0.1501-0.04261.1834-0.09691.0444-0.0523-0.14080.10840.1301-0.00840.0419-0.1407-0.07880.06070.16180.0171-0.00290.0969-0.05230.0316-11.11913.80331.485
280.5741-0.14310.32390.5966-0.13280.46850.0177-0.0944-0.01380.0234-0.00820.0557-0.0216-0.1012-0.00950.10670.00150.01420.0677-0.00810.0079-13.1-0.50525.189
290.87320.14910.17570.5312-0.22610.650.016-0.04390.12120.0406-0.00670.086-0.0474-0.1159-0.00930.11250.01760.00730.0656-0.010.0257-18.43711.10112.499
305.8831-0.06380.6592.2886-0.85482.4243-0.03610.07130.33770.02910.01870.2346-0.3128-0.19040.01750.15290.0443-0.01380.02730.00590.0876-14.55427.0838.384
311.1838-1.04990.45090.9411-0.32811.3467-0.0970.00570.29210.094-0.0131-0.2493-0.10220.09590.11010.168-0.0302-0.03120.0506-0.02360.09532.30521.12524.071
3210.9656-6.6083-0.97776.35920.69973.74160.00360.34710.3687-0.0835-0.2017-0.2342-0.46210.18420.1980.1199-0.0361-0.01650.03120.05260.16581.10531.51919.225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 6
2X-RAY DIFFRACTION2A7 - 33
3X-RAY DIFFRACTION3A34 - 75
4X-RAY DIFFRACTION4A76 - 145
5X-RAY DIFFRACTION5A146 - 214
6X-RAY DIFFRACTION6A215 - 236
7X-RAY DIFFRACTION7A237 - 277
8X-RAY DIFFRACTION8A278 - 296
9X-RAY DIFFRACTION9B-1 - 16
10X-RAY DIFFRACTION10B17 - 37
11X-RAY DIFFRACTION11B38 - 115
12X-RAY DIFFRACTION12B116 - 132
13X-RAY DIFFRACTION13B133 - 223
14X-RAY DIFFRACTION14B224 - 246
15X-RAY DIFFRACTION15B247 - 278
16X-RAY DIFFRACTION16B279 - 296
17X-RAY DIFFRACTION17C-1 - 6
18X-RAY DIFFRACTION18C7 - 33
19X-RAY DIFFRACTION19C34 - 75
20X-RAY DIFFRACTION20C76 - 145
21X-RAY DIFFRACTION21C146 - 223
22X-RAY DIFFRACTION22C224 - 247
23X-RAY DIFFRACTION23C248 - 285
24X-RAY DIFFRACTION24C286 - 296
25X-RAY DIFFRACTION25D-1 - 6
26X-RAY DIFFRACTION26D7 - 33
27X-RAY DIFFRACTION27D34 - 75
28X-RAY DIFFRACTION28D76 - 145
29X-RAY DIFFRACTION29D146 - 222
30X-RAY DIFFRACTION30D223 - 245
31X-RAY DIFFRACTION31D246 - 277
32X-RAY DIFFRACTION32D278 - 295

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