[English] 日本語
Yorodumi
- PDB-8h2c: Crystal structure of the pseudaminic acid synthase PseI from Camp... -

+
Open data


ID or keywords:

Loading...

-
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 / SAF domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more