[English] 日本語
Yorodumi
- PDB-6bvc: Crystal structure of AAC(3)-Ia in complex with coenzyme A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bvc
TitleCrystal structure of AAC(3)-Ia in complex with coenzyme A
ComponentsAminoglycoside-(3)-N-acetyltransferase
KeywordsTRANSFERASE / aminoglycoside / antibiotic / resistance / GCN5 family N-acetyltransferase / GNAT / alpha/beta protein / coenzyme A / CoA / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / Chem-PE3 / Aminoglycoside-(3)-N-acetyltransferase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.808 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Savchenko, A. / Joachimiak, A. / Satchell, K. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: To be published
Authors: Stogios, P.J.
History
DepositionDec 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoglycoside-(3)-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7858
Polymers19,4361
Non-polymers2,3497
Water3,315184
1
A: Aminoglycoside-(3)-N-acetyltransferase
hetero molecules

A: Aminoglycoside-(3)-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56916
Polymers38,8722
Non-polymers4,69814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area11600 Å2
ΔGint-66 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.028, 100.875, 53.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-342-

HOH

31A-346-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Aminoglycoside-(3)-N-acetyltransferase


Mass: 19435.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: aacC1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q53396

-
Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M NaCl, 25% PEG3350, 0.1M Na Citrate pH5.6, cryo paratone

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.81→62.21 Å / Num. obs: 19775 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.048 / Net I/σ(I): 17.3
Reflection shellResolution: 1.81→2.02 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5532 / CC1/2: 0.903 / Rpim(I) all: 0.314 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BO4

1bo4


Resolution: 1.808→50.438 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 1865 5.01 %RANDOM
Rwork0.1623 ---
obs0.1637 37209 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.808→50.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 85 184 1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021327
X-RAY DIFFRACTIONf_angle_d2.0251803
X-RAY DIFFRACTIONf_dihedral_angle_d18.827507
X-RAY DIFFRACTIONf_chiral_restr0.133196
X-RAY DIFFRACTIONf_plane_restr0.008227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8084-1.85730.29631420.28122695X-RAY DIFFRACTION99
1.8573-1.9120.30031420.25432713X-RAY DIFFRACTION100
1.912-1.97370.24371430.21742767X-RAY DIFFRACTION99
1.9737-2.04420.22531460.18792688X-RAY DIFFRACTION99
2.0442-2.12610.23111450.17272740X-RAY DIFFRACTION100
2.1261-2.22280.22421410.16452705X-RAY DIFFRACTION99
2.2228-2.340.15021430.15362717X-RAY DIFFRACTION99
2.34-2.48660.16181420.1492738X-RAY DIFFRACTION99
2.4866-2.67860.16831480.13922726X-RAY DIFFRACTION100
2.6786-2.94820.19151460.14622716X-RAY DIFFRACTION99
2.9482-3.37470.16751420.14012712X-RAY DIFFRACTION99
3.3747-4.25140.15481440.132691X-RAY DIFFRACTION99
4.2514-50.45710.20231410.17712736X-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)
14.511-0.73270.31862.53143.91427.65030.02180.1552-0.796-0.04120.0415-0.07740.77680.1799-0.04170.2389-0.00540.02720.1437-0.00660.25822.72190.864972.8232
24.93280.5046-0.72253.64661.10925.1145-0.0280.0437-0.1414-0.17160.0382-0.20810.10220.20070.00970.07050.0269-0.01190.09240.00860.130534.564312.792271.8225
32.99090.93191.29453.4438-0.25282.72830.0087-0.25190.0980.1758-0.05260.0980.1032-0.140.04940.084-0.00110.03230.13440.00750.078225.98412.341278.2037
45.4102-5.8706-1.40966.37091.52470.36610.02420.0812-0.152-0.0379-0.03330.15570.0207-0.04540.00060.1097-0.0028-0.00760.1274-0.01770.132417.737919.015869.6729
52.9232-1.38920.89815.068-1.48395.07290.08630.102-0.2389-0.2697-0.1412-0.13930.68870.36020.04590.29440.01890.0420.1755-0.03250.16427.30120.794159.6118
62.5855-1.208-0.68814.10910.39554.59980.08450.1565-0.005-0.4117-0.07890.1033-0.049-0.0080.00450.1032-0.0135-0.04010.1142-0.02310.141316.571112.93962.6941
76.1725.392.59814.89752.88483.542-0.17530.18630.0063-0.90220.1222-0.1571-0.42370.14880.01430.25330.07070.00090.22050.0230.251523.210330.745958.5453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 121 )
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 160 )
7X-RAY DIFFRACTION7chain 'A' and (resid 161 through 177 )

+
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://pdbjlvh1.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