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- PDB-2wle: Crystallographic analysis of the polysialic acid O-acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 2wle
TitleCrystallographic analysis of the polysialic acid O-acetyltransferase OatWY
ComponentsPOLYSIALIC ACID O-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ENZYME / ACETYLTRANSFERASE / LEFT-HANDED BETA HELIX
Function / homology
Function and homology information


polysialic-acid O-acetyltransferase activity / protein homotrimerization / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
: / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Polysialic acid O-acetyltransferase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP Y (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Kinetic Characterizations of the Polysialic Acid O-Acetyltransferase Oatwy from Neisseria Meningitidis.
Authors: Lee, H.J. / Rakic, B. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.
History
DepositionJun 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: POLYSIALIC ACID O-ACETYLTRANSFERASE
B: POLYSIALIC ACID O-ACETYLTRANSFERASE
C: POLYSIALIC ACID O-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9128
Polymers71,1943
Non-polymers1,7185
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-34.4 kcal/mol
Surface area32060 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.074, 94.523, 100.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 6 - 214 / Label seq-ID: 6 - 214

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA
3CC

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Components

#1: Protein POLYSIALIC ACID O-ACETYLTRANSFERASE


Mass: 23731.191 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LEFT-HANDED BETA HELIX
Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP Y (bacteria)
Strain: 406Y / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: Q93S40
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 67 TO ILE ENGINEERED RESIDUE IN CHAIN C, ASN 67 TO ILE

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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: 2.65 Å3/Da / Density % sol: 54 %
Description: STARTING MODEL WAS MY NAI SOAKING SIRAS STRUCTURE SOLVED BY SHELX-CDE.
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE, PH 4.6, 2.25 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: COPPER HOME SOURCE / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 2007 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 39161 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE

Resolution: 2.19→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.927 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24245 1966 5 %RANDOM
Rwork0.19512 ---
obs0.1975 37139 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.778 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2---0.62 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.19→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 108 215 5178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225086
X-RAY DIFFRACTIONr_bond_other_d0.0010.024545
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9656910
X-RAY DIFFRACTIONr_angle_other_deg1.295310646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89125.654214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40615895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5151516
X-RAY DIFFRACTIONr_chiral_restr0.0590.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025568
X-RAY DIFFRACTIONr_gen_planes_other00.02900
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_it0.321.53132
X-RAY DIFFRACTIONr_mcbond_other0.0961.51312
X-RAY DIFFRACTIONr_mcangle_it0.63325105
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1831954
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9634.51798
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3009 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Bmedium positional0.460.5
2Amedium positional0.490.5
3Cmedium positional0.510.5
1Bmedium thermal0.352
2Amedium thermal0.422
3Cmedium thermal0.322
LS refinement shellResolution: 2.195→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 135 -
Rwork0.259 2567 -
obs--94.57 %
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)
111.90313.16875.693616.17625.522611.3480.15331.07760.4185-0.67150.55950.71780.3473-0.8543-0.71280.45330.3363-0.14560.82480.18040.419622.23836.3421-32.0946
21.0399-0.3493-1.39222.66111.60675.0149-0.03450.24740.1828-0.25180.08550.2428-0.0347-0.4995-0.0510.1854-0.0096-0.0450.21060.06550.121528.5385-1.0613-37.3119
32.87247.54146.036938.445228.881725.5376-0.0625-0.22920.29870.7721-0.68091.40030.4499-1.45450.74340.1285-0.0021-0.02990.26280.06660.186423.3792-4.7621-29.0778
42.5856-0.4081-1.00763.63020.60873.1552-0.0230.11510.0205-0.112-0.00540.09330.091-0.20740.02830.1046-0.0378-0.02810.16510.03270.084831.2416-6.5529-32.2712
50.3052-0.1768-0.35030.91381.0324.1644-0.02780.006-0.0414-0.0696-0.01690.00120.21430.03420.04470.0814-0.02780.00370.1150.01420.081133.6954-11.6772-21.1554
62.4775-0.8557-2.08992.76761.36163.795-0.3004-0.2155-0.37430.04730.1233-0.12120.62480.2910.17710.24460.02390.05070.13660.04830.131940.826-23.8146-26.2429
714.7096-9.5673-1.639913.4729-4.71719.33680.51391.65450.7582-0.3234-0.3273-0.6720.3423-0.3493-0.18660.35890.09840.19550.46860.07860.34648.5433-26.9744-44.5324
83.0906-5.4240.455511.30182.70089.3820.17640.2355-0.0237-0.151-0.21980.39970.251-1.25460.04340.6787-0.1325-0.01131.34860.32830.56312.2765-30.473-53.0066
95.7933-0.5682-2.27722.229-1.22075.86240.1630.2521-0.0691-0.471-0.00460.3410.9239-0.9941-0.15850.7328-0.3741-0.05810.4384-0.01940.165311.0065-38.1684-47.8207
106.02310.1803-4.76980.6347-0.32136.680.32930.00020.0221-0.3828-0.113-0.07020.5989-0.5049-0.21640.6304-0.2257-0.02680.3174-0.0190.16516.6312-37.8328-44.4572
114.06130.9485-1.95831.6697-1.12663.80470.04240.1539-0.0922-0.33260.0538-0.0060.6235-0.3895-0.09620.5366-0.22630.01910.1847-0.0360.161320.4112-38.9106-36.1586
122.16611.6432-1.04931.3649-1.12821.9251-0.0457-0.0568-0.28-0.24-0.0117-0.23270.60720.00480.05740.5155-0.10080.06570.1161-0.01540.207730.9707-39.7928-30.6099
134.64012.97320.08314.7799-0.11233.795-0.0192-0.119-0.5311-0.0886-0.0087-0.57940.64410.20730.02790.6267-0.18570.00080.17790.0230.239225.8498-47.3676-19.4285
142.87984.1575-0.5757.2072-1.87263.7647-0.57010.42630.2061-1.3460.82731.33360.7396-0.7933-0.25721.0234-0.555-0.2720.43890.01411.12457.9932-53.9859-18.6822
157.02464.515-5.23298.4165-8.312711.78840.43780.35291.01290.1706-0.23361.2639-0.6856-0.6626-0.20420.3887-0.1518-0.04580.7215-0.12230.7568-9.6482-23.7075-13.3726
165.79974.0653-0.21356.67321.09411.5737-0.02570.17450.6130.0518-0.10290.66460.1284-0.55130.12860.1581-0.18180.03660.3910.0410.3395-0.9814-17.6796-11.2854
175.70283.3339-0.54476.3038-0.05572.4505-0.27630.048-0.0436-0.1910.05060.20140.2205-0.34020.22580.1875-0.13970.06060.29620.05040.23482.9313-22.0853-8.9034
183.46361.8974-0.11484.2941-0.11830.9848-0.11860.0364-0.00570.05570.06780.28970.4096-0.33120.05080.2259-0.13540.05080.24090.04470.149310.7354-25.1295-9.7325
193.5863-0.0443-0.61068.43541.63264.48670.10340.0211-0.35190.3045-0.01380.17340.5344-0.0666-0.08960.5224-0.28680.03590.24150.05690.237313.2493-48.235-12.1514
202.04051.95450.52613.35171.28072.02960.0298-0.1211-0.18850.15790.0013-0.07110.3838-0.1466-0.03110.1701-0.05740.02560.1580.04140.071725.2487-21.5619-4.7011
2121.86676.2435-1.929229.55391.04668.99920.2103-1.8405-0.46070.3997-0.1112-1.0713-0.4399-0.3952-0.09920.3581-0.06360.24010.2942-0.05280.240924.8316-11.86137.5578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 11
2X-RAY DIFFRACTION2A12 - 46
3X-RAY DIFFRACTION3A47 - 54
4X-RAY DIFFRACTION4A55 - 75
5X-RAY DIFFRACTION5A76 - 134
6X-RAY DIFFRACTION6A135 - 199
7X-RAY DIFFRACTION7A200 - 214
8X-RAY DIFFRACTION8B5 - 9
9X-RAY DIFFRACTION9B10 - 45
10X-RAY DIFFRACTION10B46 - 64
11X-RAY DIFFRACTION11B65 - 119
12X-RAY DIFFRACTION12B120 - 170
13X-RAY DIFFRACTION13B171 - 197
14X-RAY DIFFRACTION14B198 - 214
15X-RAY DIFFRACTION15C5 - 12
16X-RAY DIFFRACTION16C13 - 50
17X-RAY DIFFRACTION17C51 - 68
18X-RAY DIFFRACTION18C69 - 117
19X-RAY DIFFRACTION19C118 - 135
20X-RAY DIFFRACTION20C136 - 210
21X-RAY DIFFRACTION21C211 - 215

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