[English] 日本語
Yorodumi
- PDB-3n0s: Crystal structure of BA2930 mutant (H183A) in complex with AcCoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n0s
TitleCrystal structure of BA2930 mutant (H183A) in complex with AcCoA
ComponentsAminoglycoside N3-acetyltransferase
KeywordsTRANSFERASE / ACCOA / 2 ACYLTRANSFERASE / 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 / ACETYL COENZYME *A / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsKlimecka, M.M. / Chruszcz, M. / Porebski, P.J. / Cymborowski, M. / Anderson, W.F. / 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
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: 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
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,60611
Polymers121,0804
Non-polymers3,5257
Water6,738374
1
A: Aminoglycoside N3-acetyltransferase
B: Aminoglycoside N3-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4226
Polymers60,5402
Non-polymers1,8824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-30 kcal/mol
Surface area22730 Å2
MethodPISA
2
D: Aminoglycoside N3-acetyltransferase
C: Aminoglycoside N3-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1845
Polymers60,5402
Non-polymers1,6433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-29 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.036, 109.441, 74.048
Angle α, β, γ (deg.)90.00, 111.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 1 - 263 / Label seq-ID: 4 - 266

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BD
3CC
4DB

-
Components

#1: Protein
Aminoglycoside N3-acetyltransferase


Mass: 30270.102 Da / Num. of mol.: 4 / Mutation: H183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: aacC7, BA_2930, GBAA2930, GBAA_2930 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)
References: UniProt: Q81P86, UniProt: A0A3P1UCA6*PLUS, aminoglycoside 3-N-acetyltransferase
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 17%w/v PEG 3350, 0.18Molal MgCl2, 1%w/v CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2010 / Details: Be Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 57925 / Num. obs: 57925 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.487 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3KZL

3kzl


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.689 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22794 2907 5.1 %RANDOM
Rwork0.17299 ---
obs0.17583 54459 99.04 %-
all-54459 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.489 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å21.07 Å2
2---1.82 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 221 374 8855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0228705
X-RAY DIFFRACTIONr_bond_other_d0.0020.025846
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.97911827
X-RAY DIFFRACTIONr_angle_other_deg1.4123.00314161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15951062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48624.29359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.612151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6521552
X-RAY DIFFRACTIONr_chiral_restr0.1140.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219465
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021651
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_it0.9841.55306
X-RAY DIFFRACTIONr_mcbond_other0.1971.52154
X-RAY DIFFRACTIONr_mcangle_it1.8128607
X-RAY DIFFRACTIONr_scbond_it3.08833399
X-RAY DIFFRACTIONr_scangle_it4.7354.53220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1526medium positional0.290.5
B1526medium positional0.30.5
C1526medium positional0.240.5
D1526medium positional0.250.5
A1894loose positional0.725
B1894loose positional0.735
C1894loose positional0.675
D1894loose positional0.665
A1526medium thermal0.772
B1526medium thermal0.782
C1526medium thermal0.872
D1526medium thermal0.792
A1894loose thermal0.9810
B1894loose thermal1.0110
C1894loose thermal0.9710
D1894loose thermal0.9210
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 205 -
Rwork0.223 3928 -
obs--96.61 %
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)
11.19280.14620.42281.76340.51560.7349-0.06760.08040.1287-0.0350.00080.2535-0.1027-0.12750.06670.1421-0.0065-0.10750.28170.02010.1465-3.539.21436.314
20.9966-0.37590.31310.9657-0.05020.8807-0.0437-0.00090.00860.06340.0275-0.07230.01670.07480.01620.1078-0.0001-0.08380.22630.00970.082421.58-9.45543.725
30.87130.33340.21732.16060.59970.686-0.0470.0910.04710.02910.02270.3172-0.0415-0.06730.02430.14-0.0036-0.08240.27340.01220.118610.3629.2781.218
41.0074-0.24810.18710.83620.15850.6997-0.11080.02110.00480.08060.086-0.08620.00160.10910.02480.15080.0103-0.08460.25670.01720.075436.024-8.03610.164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 263
2X-RAY DIFFRACTION2B1 - 263
3X-RAY DIFFRACTION3C1 - 263
4X-RAY DIFFRACTION4D1 - 263

+
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