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- PDB-8h2c: Crystal structure of the pseudaminic acid synthase PseI from Camp... -

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Basic information

Entry
Database: PDB / ID: 8h2c
TitleCrystal structure of the pseudaminic acid synthase PseI from Campylobacter jejuni
ComponentsPseudaminic acid synthase
KeywordsBIOSYNTHETIC PROTEIN / Pseudaminic acid synthase / TIM barrel fold / Type III antifreeze-like domain / condensation reaction
Function / homology
Function and homology information


pseudaminic acid synthase / carbohydrate biosynthetic process / transferase activity
Similarity search - Function
Pseudaminic acid biosynthesis, PseI / N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF domain / SAF / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / Pseudaminic acid synthase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSong, W.S. / Park, M.A. / Ki, D.U. / Yoon, S.I.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
National Research Foundation (NRF, Korea)2019R1I1A1A01047141 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural analysis of the pseudaminic acid synthase PseI from Campylobacter jejuni.
Authors: Song, W.S. / Park, M.A. / Ki, D.U. / Yoon, S.I.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudaminic acid synthase
B: Pseudaminic acid synthase
C: Pseudaminic acid synthase
D: Pseudaminic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,1758
Polymers156,9554
Non-polymers2204
Water86548
1
A: Pseudaminic acid synthase
B: Pseudaminic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5874
Polymers78,4782
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-45 kcal/mol
Surface area27400 Å2
MethodPISA
2
C: Pseudaminic acid synthase
D: Pseudaminic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5874
Polymers78,4782
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-41 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.805, 176.805, 99.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 and (name N or name...
21(chain B and ((resid 2 and (name N or name...
31(chain C and (resid 2 through 4 or (resid 5...
41(chain D and (resid 2 through 8 or (resid 9...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLNGLN(chain A and ((resid 2 and (name N or name...AA28
12METMETPHEPHE(chain A and ((resid 2 and (name N or name...AA1 - 3427 - 348
13METMETPHEPHE(chain A and ((resid 2 and (name N or name...AA1 - 3427 - 348
14METMETPHEPHE(chain A and ((resid 2 and (name N or name...AA1 - 3427 - 348
15METMETPHEPHE(chain A and ((resid 2 and (name N or name...AA1 - 3427 - 348
21GLNGLNGLNGLN(chain B and ((resid 2 and (name N or name...BB28
22METMETPHEPHE(chain B and ((resid 2 and (name N or name...BB1 - 3427 - 348
23METMETPHEPHE(chain B and ((resid 2 and (name N or name...BB1 - 3427 - 348
24METMETPHEPHE(chain B and ((resid 2 and (name N or name...BB1 - 3427 - 348
25METMETPHEPHE(chain B and ((resid 2 and (name N or name...BB1 - 3427 - 348
31GLNGLNGLYGLY(chain C and (resid 2 through 4 or (resid 5...CC2 - 48 - 10
32ASNASNASNASN(chain C and (resid 2 through 4 or (resid 5...CC511
33METMETPHEPHE(chain C and (resid 2 through 4 or (resid 5...CC1 - 3427 - 348
34METMETPHEPHE(chain C and (resid 2 through 4 or (resid 5...CC1 - 3427 - 348
35METMETPHEPHE(chain C and (resid 2 through 4 or (resid 5...CC1 - 3427 - 348
36METMETPHEPHE(chain C and (resid 2 through 4 or (resid 5...CC1 - 3427 - 348
41GLNGLNTHRTHR(chain D and (resid 2 through 8 or (resid 9...DD2 - 88 - 14
42ASPASPLYSLYS(chain D and (resid 2 through 8 or (resid 9...DD9 - 1015 - 16
43GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
44GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
45GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
46GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
47GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
48GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
49GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
410GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
411GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
412GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348
413GLNGLNPHEPHE(chain D and (resid 2 through 8 or (resid 9...DD2 - 3428 - 348

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Components

#1: Protein
Pseudaminic acid synthase


Mass: 39238.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: pseI, FRQ26_09070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6C7NV50, pseudaminic acid synthase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, lithium sulfate, Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 35895 / % possible obs: 97.9 % / Redundancy: 8.3 % / CC1/2: 0.981 / Net I/σ(I): 11
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1787 / CC1/2: 0.39 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alpha fold2 model

Resolution: 2.9→30 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 1741 5.03 %
Rwork0.2446 32862 -
obs0.2472 34603 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.73 Å2 / Biso mean: 46.8057 Å2 / Biso min: 4.2 Å2
Refinement stepCycle: final / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10251 0 4 48 10303
Biso mean--39.17 23.66 -
Num. residues----1357
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5697X-RAY DIFFRACTION10.702TORSIONAL
12B5697X-RAY DIFFRACTION10.702TORSIONAL
13C5697X-RAY DIFFRACTION10.702TORSIONAL
14D5697X-RAY DIFFRACTION10.702TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.98530.41491390.3401272598
2.9853-3.08150.36031490.3211272099
3.0815-3.19160.36551300.2944274899
3.1916-3.31920.32471430.2699273498
3.3192-3.470.28491380.274274198
3.47-3.65260.34471330.2653271598
3.6526-3.8810.37531290.2951269395
3.881-4.17990.28081610.2356262694
4.1799-4.59910.27281480.2258266094
4.5991-5.26140.22431500.1929267594
5.2614-6.61640.26791610.2175281298
6.6164-29.4690.23711600.1883013100
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)
14.21910.41150.15442.86340.28142.0062-0.1595-0.60630.078-0.27-0.1027-0.3621-0.20380.02050.25650.32670.03850.12480.3670.01660.273763.824943.128110.0248
23.37380.79480.44042.46311.58012.0246-0.1380.0037-0.2054-0.01580.1768-0.43780.04350.315-0.00420.26580.00670.00240.4098-0.04780.358271.580255.60316.8258
31.94881.2708-0.61555.2377-1.58444.28230.1518-0.20540.22-0.1277-0.18750.1212-0.1005-0.0417-0.04370.15460.01710.0230.3038-0.05210.345252.589154.887220.9273
46.8881-0.2622-2.02973.09610.78663.4483-0.1876-0.1811-0.39340.50410.0136-0.71470.81460.44460.17210.36030.0828-0.01170.35480.09410.417159.77636.49718.922
54.8053.29931.01995.20581.05771.1379-0.202-0.07390.209-0.28180.05350.68250.2170.00360.19030.31480.04550.01640.3344-0.02510.238111.958415.255414.7496
63.03250.30160.97420.7090.24682.71460.1789-0.01380.4304-0.0608-0.4285-0.29170.10350.18220.19220.4447-0.07240.01640.46420.22740.526736.123819.216537.0915
71.93310.06711.54460.80981.02382.82220.2878-0.1964-0.10170.3441-0.04780.00220.4032-0.1339-0.270.5254-0.01430.06560.29270.05250.348224.4858.888330.1691
82.86811.6249-0.23751.8963-0.41351.94780.0125-0.1481-0.33190.0999-0.073-0.07250.1190.00740.04410.3480.01620.01380.20890.0540.329731.91626.973826.1495
93.73492.05420.16783.84211.84720.93680.4934-0.36680.53580.0271-0.1232-0.0614-0.45580.2199-0.35610.4394-0.0250.13230.4436-0.00280.403365.89369.958129.6632
101.4526-0.9706-2.8843.60550.03326.489-0.37650.3139-0.3698-0.72270.5203-0.3627-0.10520.1761-0.09180.4613-0.07980.0480.4155-0.24160.455171.667522.7799-49.295
113.52431.8973-1.88291.7755-0.60772.36630.25060.73480.1408-0.53830.1199-0.021-0.1072-0.1206-0.31290.50190.04060.05690.42010.03820.281676.795337.8299-48.6696
122.9434-0.2435-0.39792.9001-0.79373.2181-0.03530.2239-0.3235-0.3130.0113-0.461-0.04330.1136-0.00150.2963-0.0280.07490.2402-0.00160.41372.189127.5114-35.6399
136.49972.9698-6.17991.2029-1.9254.7812-0.10090.07550.0396-0.07610.0469-0.04360.09250.0683-0.00020.29360.0464-0.00840.38930.07420.397540.9745.692-13.4808
142.9642.4243-0.76142.03150.19591.10850.188-0.1581-0.13820.2961-0.3363-0.40490.07640.16950.15280.369-0.0048-0.04160.28820.11710.499257.90833.7763-2.9044
151.81120.7189-0.65491.7419-0.53913.19460.07830.131-0.10010.1487-0.0511-0.2226-0.0333-0.0891-0.04680.2437-0.0286-0.0290.19040.02580.416557.322913.9925-14.505
162.76511.6657-0.69524.7032-1.73920.83480.286-0.08990.2754-0.1606-0.1132-0.3314-0.17560.28-0.18610.41860.00570.14540.3466-0.03890.338183.469852.7355-41.1278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 133 )A49 - 133
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 210 )A134 - 210
4X-RAY DIFFRACTION4chain 'A' and (resid 211 through 267 )A211 - 267
5X-RAY DIFFRACTION5chain 'A' and (resid 268 through 342 )A268 - 342
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 48 )B1 - 48
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 119 )B49 - 119
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 267 )B120 - 267
9X-RAY DIFFRACTION9chain 'B' and (resid 268 through 342 )B268 - 342
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 48 )C1 - 48
11X-RAY DIFFRACTION11chain 'C' and (resid 49 through 168 )C49 - 168
12X-RAY DIFFRACTION12chain 'C' and (resid 169 through 249 )C169 - 249
13X-RAY DIFFRACTION13chain 'C' and (resid 250 through 342 )C250 - 342
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 133 )D2 - 133
15X-RAY DIFFRACTION15chain 'D' and (resid 134 through 267 )D134 - 267
16X-RAY DIFFRACTION16chain 'D' and (resid 268 through 342 )D268 - 342

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