[English] 日本語
Yorodumi
- PDB-3e4f: Crystal structure of BA2930- a putative aminoglycoside N3-acetylt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e4f
TitleCrystal structure of BA2930- a putative aminoglycoside N3-acetyltransferase from Bacillus anthracis
ComponentsAminoglycoside N3-acetyltransferase
KeywordsTRANSFERASE / N3-acetyltransferase / Bacillus anthracis / antrax / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / CITRIC ACID / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKlimecka, M.M. / Chruszcz, M. / Skarina, T. / Onopryienko, O. / Cymborowski, M. / Savchenko, A. / Edwards, A. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis.
Authors: Klimecka, M.M. / Chruszcz, M. / Font, J. / Skarina, T. / Shumilin, I. / Onopryienko, O. / Porebski, P.J. / Cymborowski, M. / Zimmerman, M.D. / Hasseman, J. / Glomski, I.J. / Lebioda, L. / ...Authors: Klimecka, M.M. / Chruszcz, M. / Font, J. / Skarina, T. / Shumilin, I. / Onopryienko, O. / Porebski, P.J. / Cymborowski, M. / Zimmerman, M.D. / Hasseman, J. / Glomski, I.J. / Lebioda, L. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoglycoside N3-acetyltransferase
B: Aminoglycoside N3-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8986
Polymers60,1302
Non-polymers7684
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-30 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.313, 108.046, 132.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Aminoglycoside N3-acetyltransferase


Mass: 30064.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: aacC7, BA_2930, GBAA2930 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q81P86, UniProt: A0A1J9VPY4*PLUS
#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M Na citrate, 0.1M HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 36337 / Num. obs: 36337 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 38.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1790 / Rsym value: 0.496 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.005 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.181 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22593 1806 5 %RANDOM
Rwork0.17269 ---
all0.1753 34404 --
obs0.1753 34404 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.853 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20 Å20 Å2
2---0.88 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 52 293 4391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224224
X-RAY DIFFRACTIONr_bond_other_d0.0030.022818
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9615749
X-RAY DIFFRACTIONr_angle_other_deg2.98736894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5035529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55824.205176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84115707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7521525
X-RAY DIFFRACTIONr_chiral_restr0.090.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214702
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02817
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7951.52621
X-RAY DIFFRACTIONr_mcbond_other0.221.51068
X-RAY DIFFRACTIONr_mcangle_it1.42624262
X-RAY DIFFRACTIONr_scbond_it2.8231603
X-RAY DIFFRACTIONr_scangle_it4.0894.51487
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 112 -
Rwork0.169 2448 -
obs--97.52 %
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)
11.25630.02320.30570.81090.33991.58380.03750.11420.0391-0.1679-0.0530.0154-0.0461-0.07640.0155-0.06980.0055-0.0167-0.0057-0.00790.01342.06468.875-7.712
25.86162.1171-1.82726.8776-1.44043.2480.0634-0.09350.07160.34740.00410.340.3262-0.172-0.06740.24480.00150.0211-0.17890.0058-0.1175.00537.9699.935
31.5459-0.49040.32871.9886-0.41583.41450.01450.0135-0.1018-0.1584-0.0077-0.19120.29020.2494-0.0069-0.0990.02320.005-0.0473-0.01550.02312.82358.9242.078
40.9591-0.5254-0.01511.0655-0.09622.0754-0.0028-0.0867-0.06630.07090.04740.07660.1197-0.0635-0.0446-0.0898-0.0069-0.0072-0.0340.01330.01862.09463.85112.261
50.46320.4189-0.12291.3103-0.44762.837-0.0870.1237-0.09080.3932-0.001-0.02330.5006-0.23880.0880.1537-0.01470.0409-0.1344-0.0507-0.046812.28936.29-9.51
62.603-2.9530.74035.1283-0.43570.9548-0.0260.2365-0.08790.0038-0.08890.2026-0.0352-0.22840.1148-0.07120.0229-0.00580.0236-0.0279-0.10964.79657.371-20.77
70.7333-0.448-0.42171.58260.46592.13910.00310.3136-0.0103-0.0885-0.0678-0.09060.0554-0.16440.0647-0.1010.01090.00240.0485-0.0459-0.079512.6548.279-28.547
81.7393-0.0114-0.39271.8576-1.99986.53220.00730.4384-0.2467-0.0025-0.03210.31711.2406-0.97420.02470.0901-0.19180.01370.0373-0.1683-0.03255.67931.193-27.983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 733 - 73
2X-RAY DIFFRACTION2AA74 - 9974 - 99
3X-RAY DIFFRACTION3AA100 - 152100 - 152
4X-RAY DIFFRACTION4AA153 - 264153 - 264
5X-RAY DIFFRACTION5BB4 - 734 - 73
6X-RAY DIFFRACTION6BB74 - 12774 - 127
7X-RAY DIFFRACTION7BB128 - 218128 - 218
8X-RAY DIFFRACTION8BB219 - 264219 - 264

+
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