[English] 日本語
Yorodumi
- PDB-8fbu: Crystal structure of Cryptosporidium parvum N-myristoyltransferas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fbu
TitleCrystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and Compound-2
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE/INHIBITOR / NMT / inhibitor / Myristoyl-CoA / MyrCoA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm
Similarity search - Function
Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
TETRADECANOYL-COA / TRIETHYLENE GLYCOL / Chem-XOL / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStaker, B.L. / Fenwick, M.K. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI155536 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Identification of and Structural Insights into Hit Compounds Targeting N -Myristoyltransferase for Cryptosporidium Drug Development.
Authors: Fenwick, M.K. / Reers, A.R. / Liu, Y. / Zigweid, R. / Sankaran, B. / Shin, J. / Hulverson, M.A. / Hammerson, B. / Fernandez Alvaro, E. / Myler, P.J. / Kaushansky, A. / Van Voorhis, W.C. / Fan, E. / Staker, B.L.
History
DepositionNov 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Sep 4, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,96913
Polymers101,4342
Non-polymers3,53511
Water10,395577
1
A: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7447
Polymers50,7171
Non-polymers2,0276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2256
Polymers50,7171
Non-polymers1,5085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.777, 88.228, 98.060
Angle α, β, γ (deg.)90.00, 97.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 50717.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd3_320
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5CV46

-
Non-polymers , 8 types, 588 molecules

#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XOL / (2M)-2-[2-(piperazin-1-yl)phenyl]-N-(1,3-thiazol-2-yl)-1H-benzimidazole-4-carboxamide


Mass: 404.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N6OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 1.0 mM compound at 4C for 30 min, then mixed with 1:1 with 100 mM BisTris-HCl pH 6. ...Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 1.0 mM compound at 4C for 30 min, then mixed with 1:1 with 100 mM BisTris-HCl pH 6.5 and 27.5% PEG 3350. Protein buffer is 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide. Crystals are harvested using crystallant plus 25% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59810 / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.23 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 1.44 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2994 / CC1/2: 0.504 / CC star: 0.819 / Rpim(I) all: 0.506 / Rrim(I) all: 0.927 / Χ2: 0.778 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.20.1.4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.37 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2926 4.9 %
Rwork0.1552 --
obs0.1577 59728 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 232 577 7822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127751
X-RAY DIFFRACTIONf_angle_d1.12210519
X-RAY DIFFRACTIONf_dihedral_angle_d18.7712912
X-RAY DIFFRACTIONf_chiral_restr0.061122
X-RAY DIFFRACTIONf_plane_restr0.0091338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.2762800.20821539X-RAY DIFFRACTION55
2.02-2.050.24131450.1952744X-RAY DIFFRACTION98
2.05-2.090.26921470.19352738X-RAY DIFFRACTION97
2.09-2.130.25081320.1932761X-RAY DIFFRACTION98
2.13-2.170.23681490.19182747X-RAY DIFFRACTION97
2.17-2.220.26051240.18362757X-RAY DIFFRACTION97
2.22-2.270.2521390.18822749X-RAY DIFFRACTION96
2.27-2.330.21641330.17222701X-RAY DIFFRACTION96
2.33-2.390.23361310.16992755X-RAY DIFFRACTION97
2.39-2.460.26441550.16832675X-RAY DIFFRACTION95
2.46-2.540.24711510.16132698X-RAY DIFFRACTION96
2.54-2.630.25151350.16122712X-RAY DIFFRACTION96
2.63-2.740.21581220.15712713X-RAY DIFFRACTION95
2.74-2.860.21951190.16432767X-RAY DIFFRACTION96
2.86-3.010.23361480.16452748X-RAY DIFFRACTION97
3.01-3.20.19811470.15512780X-RAY DIFFRACTION99
3.2-3.450.18951360.14032826X-RAY DIFFRACTION99
3.45-3.80.18051610.13842843X-RAY DIFFRACTION100
3.8-4.350.16631720.12282795X-RAY DIFFRACTION99
4.35-5.470.17121450.12542865X-RAY DIFFRACTION99
5.47-35.370.20331550.17012889X-RAY DIFFRACTION99
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)
11.6267-0.194-0.61382.1349-0.39372.4019-0.05330.0162-0.12080.06040.0542-0.03170.10630.08130.00650.1521-0.0267-0.0160.1385-0.02820.1513.4719-2.259740.5788
21.7275-0.24610.35231.49230.29513.3274-0.0047-0.07750.2567-0.01870.00590.1219-0.321-0.44280.02770.16850.01140.00540.1520.00630.22922.544724.530246.3747
31.6615-0.4914-0.15211.80360.53061.54640.04330.10690.1318-0.2197-0.01430.0147-0.2638-0.0498-0.02510.1978-0.024-0.00690.16030.02710.14049.412917.218436.0485
42.2763-0.37370.09991.6814-0.33961.6817-0.02210.12540.1018-0.28310.0235-0.02060.04450.1512-0.00610.2296-0.0582-0.00190.1713-0.02170.134711-13.8866-2.8043
52.9523-0.2131.88880.0447-0.03262.01020.0406-0.1548-0.01950.2849-0.0999-0.20920.03810.05140.05880.2417-0.0030.05130.2066-0.01090.120415.7295-22.7924.8562
61.2789-0.66410.4571.8681-0.53121.3992-0.041-0.1118-0.00170.06310.05780.24050.0648-0.0867-0.01930.1994-0.03440.03480.1648-0.02230.16930.4472-20.714614.5636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 220 )
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 288 )
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 466 )
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 212 )
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 271 )
6X-RAY DIFFRACTION6chain 'B' and (resid 272 through 466 )

+
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