[English] 日本語
Yorodumi
- PDB-6wqc: Crystal structure of VipF from Legionella hackeliae in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wqc
TitleCrystal structure of VipF from Legionella hackeliae in complex with CoA
ComponentsN-terminal acetyltransferase, GNAT family
KeywordsTRANSFERASE / acetyltransferase / coenzyme A / CoA / legionella hackeliae / legionella pneumophila / effector / VipF
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / N-terminal acetyltransferase, GNAT family
Similarity search - Component
Biological speciesLegionella hackeliae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å
AuthorsStogios, P.J. / Skarina, T. / Wawrzak, Z. / Sandoval, J. / Di Leo, R. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of VipF from Legionella hackeliae in complex with CoA
Authors: Stogios, P.J.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-terminal acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6303
Polymers34,0951
Non-polymers1,5352
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.062, 36.659, 59.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein N-terminal acetyltransferase, GNAT family / vipF


Mass: 34095.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella hackeliae (bacteria) / Gene: vipF, LHA_0223 / Plasmid: pMCSG68SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A0A8UKD4
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1 M ammonium citrate pH 7.0, 0.1 M Bis-Tris pH 7, 0.2 M ammonium acetate, Cryo: paratone

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. obs: 15984 / % possible obs: 95 % / Redundancy: 11.6 % / Biso Wilson estimate: 27.58 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.028 / Net I/σ(I): 24.76
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2 / Num. unique obs: 660 / CC1/2: 0.822 / Rpim(I) all: 0.248

-
Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.34→29.9 Å / SU ML: 0.2738 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1313 4.97 %RANDOM
Rwork0.1825 25083 --
obs0.1849 15241 85.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.4 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 96 113 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072535
X-RAY DIFFRACTIONf_angle_d2.10383463
X-RAY DIFFRACTIONf_chiral_restr0.1207383
X-RAY DIFFRACTIONf_plane_restr0.0073435
X-RAY DIFFRACTIONf_dihedral_angle_d4.44432064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.430.3371720.25741378X-RAY DIFFRACTION41.87
2.43-2.540.3707970.24511966X-RAY DIFFRACTION61.05
2.54-2.680.27921380.23222558X-RAY DIFFRACTION78.39
2.68-2.840.31551590.23983050X-RAY DIFFRACTION91.97
2.84-3.060.29631700.23173187X-RAY DIFFRACTION97.9
3.06-3.370.22081720.20553230X-RAY DIFFRACTION98.78
3.37-3.860.22031690.15433198X-RAY DIFFRACTION99.5
3.86-4.860.17431630.12873272X-RAY DIFFRACTION99.77
4.86-29.90.19181730.16693244X-RAY DIFFRACTION98.84
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)
14.48592375048-0.7699197414031.219744820853.48106285411-0.1603016328932.324700940230.1768380341780.178483656889-0.154472579099-0.1612654702480.0313826356457-0.491991524710.0716941281750.132578238691-0.1704226008040.1395551940510.02326010039030.0362818404840.1770226516480.000607703712160.414915506546157.7242592271.9438517448639.1441079015
21.31284821120.170488860381-1.114257114162.374770938180.2114377287252.715676534970.04717349115820.01416245664010.06075974995960.108843041384-0.1679485566560.1252125067280.147400031631-0.07741677299940.115859710770.2039313239920.0220505666943-0.02954557479120.1782634440020.01592100890240.0920597577445127.023738086-4.811410529645.6834576645
32.00264940059-0.1853486827340.240626738562.357873319680.1758264343392.97587070161-0.04334228476450.113332900855-0.0286750004860.134495297897-0.0835187076552-0.04181158963880.2240640968040.1177372714960.1146126958490.2449977875880.003249273656630.0172826047450.1555228740790.008550530387130.0646581213358128.197677101-8.040188966546.3419460915
46.44578991527-0.774294679059-4.56158237952.738219676930.1339734046946.489221891780.1016603110250.388678766430.495961969871-0.2286895510670.0242661537043-0.4912925476930.1141623817210.0870081350752-0.2188942845250.2276206151170.0110960183903-0.02231231404670.1809521205220.04508926207970.166040527297143.3579245965.1185199865134.3233076987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 256 )
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 290 )

+
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