[English] 日本語
Yorodumi
- PDB-6mmz: Crystal structure of meta-AAC0038, an environmental aminoglycosid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mmz
TitleCrystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme
ComponentsAminoglycoside N(3)-acetyltransferase
KeywordsTRANSFERASE / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / METAGENOME / SOIL / COENZYME A / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsStogios, P.J. / Skarina, T. / Xu, Z. / Yim, V. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / 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: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 26, 2020Group: Database references / Category: pdbx_database_related
Revision 1.3Apr 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase
B: Aminoglycoside N(3)-acetyltransferase
C: Aminoglycoside N(3)-acetyltransferase
D: Aminoglycoside N(3)-acetyltransferase
E: Aminoglycoside N(3)-acetyltransferase
F: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,39630
Polymers173,3336
Non-polymers2,06324
Water1,874104
1
A: Aminoglycoside N(3)-acetyltransferase
B: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3548
Polymers57,7782
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aminoglycoside N(3)-acetyltransferase
D: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52111
Polymers57,7782
Non-polymers7439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Aminoglycoside N(3)-acetyltransferase
F: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52111
Polymers57,7782
Non-polymers7439
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.761, 158.124, 143.440
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

-
Components

#1: Protein
Aminoglycoside N(3)-acetyltransferase


Mass: 28888.826 Da / Num. of mol.: 6 / Mutation: H29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: A0A059X981, aminoglycoside 3-N-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.5 M ammonium sulfate, 0.1 M bis-tris propane pH 7, 10 mM gentamicin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→19.75 Å / Num. obs: 35143 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.964 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.142 / Net I/σ(I): 6.3
Reflection shellResolution: 3.3→3.46 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4652 / CC1/2: 0.809 / Rpim(I) all: 0.395 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HT0

5ht0


Resolution: 3.3→19.75 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 1646 4.69 %RANDOM
Rwork0.2037 ---
obs0.2064 35122 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11977 0 104 104 12185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212345
X-RAY DIFFRACTIONf_angle_d0.55216789
X-RAY DIFFRACTIONf_dihedral_angle_d15.4184477
X-RAY DIFFRACTIONf_chiral_restr0.0431798
X-RAY DIFFRACTIONf_plane_restr0.0032204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.39660.38861470.29562758X-RAY DIFFRACTION100
3.3966-3.50570.34091310.27042790X-RAY DIFFRACTION100
3.5057-3.63020.31281330.24632771X-RAY DIFFRACTION100
3.6302-3.77460.28481310.22532800X-RAY DIFFRACTION100
3.7746-3.94510.31511280.22262804X-RAY DIFFRACTION100
3.9451-4.15130.26431210.20492769X-RAY DIFFRACTION100
4.1513-4.40870.24681580.18872781X-RAY DIFFRACTION100
4.4087-4.74470.22321530.17312787X-RAY DIFFRACTION100
4.7447-5.21420.21491310.16462771X-RAY DIFFRACTION100
5.2142-5.95060.23461250.18222826X-RAY DIFFRACTION100
5.9506-7.43020.21971600.19042776X-RAY DIFFRACTION100
7.4302-19.75150.21441280.17362843X-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)
11.87390.6544-1.20611.64640.32691.79120.1847-0.1917-0.06310.3798-0.1594-0.25590.4610.8157-0.02560.24960.1831-0.05850.6794-0.01660.4419116.2275-15.7985300.6189
25.9622-5.6578-1.13845.51031.80734.2805-0.5885-1.0393-0.48990.39810.93541.1581.0346-0.0197-0.29140.34770.04980.07540.41670.09770.847385.3907-3.381300.5627
31.4439-0.18430.49712.4029-0.34711.35360.1432-0.2333-0.1466-0.0370.0790.21120.48160.3269-0.23050.37360.1363-0.02240.307-0.02930.336698.362-21.9467299.7235
45.013-0.24020.38073.12620.21412.40310.1785-0.4287-0.1428-0.09110.11210.256-0.48480.4037-0.26010.2485-0.04750.00970.2922-0.02850.296897.320211.9904299.1439
53.7528-2.8606-3.55394.36822.48914.1729-0.4006-1.61851.19561.33041.0868-1.14770.03570.29-0.66560.59460.0431-0.01790.8684-0.28850.8213127.8607-0.5614304.3529
62.68870.37230.78722.26131.0070.59990.2896-0.18240.3357-0.43060.1588-0.1098-0.41180.6763-0.35750.3647-0.18190.03190.502-0.16980.41113.76169.776294.9057
71.4038-0.8112-0.54091.32390.34081.06030.0036-0.65850.53610.06330.3994-0.5469-0.27870.9484-0.25740.3626-0.29280.07960.7413-0.24990.5393115.826421.922304.1092
84.9995-0.9460.98727.4476-3.49215.2261-0.2473-0.20120.5440.4816-0.098-0.7303-0.41770.58110.28520.4611-0.0735-0.03840.455-0.02320.284120.444950.8338326.3038
91.25891.5565-1.21273.8415-0.36344.5824-0.0218-0.33110.04170.1485-0.03360.43770.3528-0.363-0.00360.4638-0.1147-0.14830.4583-0.04670.2182108.498939.3489326.9653
102.8745-1.85523.07567.9221-3.06013.45930.6062-1.5754-0.4293-0.38770.24651.1554-0.267-0.2604-0.76550.6324-0.2759-0.05230.7650.15320.452988.954734.5018324.2117
112.72740.38821.46750.98570.62883.79820.0804-0.2066-0.20780.3787-0.0873-0.15960.1665-0.2413-0.00730.5469-0.1233-0.01530.35080.03760.3365110.293336.6067328.9726
125.7529-1.0385-3.96093.4373-2.45245.8201-0.1642-0.2661-0.66621.2858-0.04570.3950.9892-0.54940.17181.3811-0.2525-0.04280.5563-0.0790.354106.594330.2352345.6128
134.38350.53090.66413.1207-1.07254.44290.2354-0.1041-0.66270.62450.11980.37830.8854-0.3302-0.21150.5557-0.40690.09950.5563-0.0390.489494.208626.545329.2792
143.3596-0.14660.43432.9671-0.60671.75880.2101-0.4558-0.04240.5179-0.4095-0.40790.8255-0.37630.23231.1822-0.12640.02270.72520.0590.3626108.642140.6698347.6952
154.30224.4686-1.04797.106-2.52239.78560.0682-0.3260.71861.5351-0.6131-0.4951-0.99091.2230.42290.5001-0.1559-0.08580.5211-0.1130.495121.703149.2663338.5644
162.2883-0.4995-4.22573.68970.21127.93930.2576-0.9507-0.29970.6791-0.073-0.10781.01670.0105-0.04031.115-0.1818-0.11810.9280.01490.2811113.067732.9795351.5019
173.7853-0.5582-0.80643.5714-0.77345.3144-0.0809-0.1625-0.07780.02270.45620.22780.4829-0.6836-0.22780.3585-0.188-0.02040.53150.04730.406290.927847.4377310.1973
188.97763.57825.4692.53313.0714.13460.2294-0.04961.18340.8716-0.85060.0359-0.0928-0.07580.58690.6089-0.29310.06430.4488-0.03920.588119.275759.8269312.0788
192.32690.5555-1.12291.7483-2.7094.18880.13970.0217-0.01740.05320.02260.36460.4211-0.4058-0.13630.3595-0.1864-0.02220.3401-0.01890.334104.300251.1951303.8524
200.87910.1801-0.05011.8609-0.95072.0985-0.01630.14110.24-0.02470.27340.2769-0.0274-0.7439-0.22020.2514-0.064-0.02230.52110.0690.37697.078763.0361298.7104
213.90961.4111-0.8285.7434-3.41044.0178-0.15070.0882-0.4751-0.64580.3178-0.459-0.29480.8223-0.12290.6406-0.27460.1140.7376-0.090.3388127.274224.3962248.0161
220.4772-0.1398-0.90294.74890.11361.71460.0438-0.0084-0.0855-0.4031-0.1050.4562-0.1835-0.21040.23470.767-0.57070.13950.6081-0.08670.5207115.329736.1659245.2078
234.2241-0.36490.13444.2677-0.33470.3164-0.62851.2906-0.481-0.54850.45310.8938-0.37270.2710.24691.0332-0.497-0.11330.5664-0.05120.611695.940340.3371244.65
242.4228-0.6237-0.08282.6329-0.86110.9480.09680.3653-0.015-0.42650.1071-0.015-0.24920.0245-0.14030.8698-0.57730.03930.4633-0.02790.4051114.906939.8342246.0881
251.4211-0.6863-0.25671.6828-0.72890.55610.07390.35620.2024-0.34950.08950.1385-0.10290.0086-0.17150.9491-0.40320.02740.76140.01990.4421113.199443.3916235.7973
260.9611-0.48860.24011.3-0.29532.599-0.2228-0.01990.0415-0.54340.502-0.456-0.2063-0.1824-0.21011.1843-0.38880.12260.8043-0.04620.381123.863135.2476226.5715
273.97370.67430.33971.60920.3432.2937-0.08030.53510.1150.00460.17460.1636-1.11280.4167-0.00050.7248-0.19270.01450.32570.01680.388593.867128.7351259.0006
285.36942.83280.94881.7405-0.43223.6141.1342-0.3744-1.5815-0.4633-0.20360.36110.32850.5625-0.67740.6735-0.2095-0.2750.5519-0.05960.8036123.42113.3566261.0337
292.3392-0.00170.94833.7444-0.76113.04020.24540.0948-0.0981-0.2938-0.005-0.0837-0.43690.6267-0.17470.6775-0.36120.02380.3484-0.06660.374107.742626.1236264.1421
301.78780.7341-0.35281.20170.1471.7631-0.017-0.0385-0.0866-0.13070.0717-0.1722-0.39540.2306-0.03180.3132-0.10630.00650.2399-0.01710.2851100.89212.8636271.7849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 262 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 85 )
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 142 )
7X-RAY DIFFRACTION7chain 'B' and (resid 143 through 262 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 51 )
9X-RAY DIFFRACTION9chain 'C' and (resid 52 through 69 )
10X-RAY DIFFRACTION10chain 'C' and (resid 70 through 88 )
11X-RAY DIFFRACTION11chain 'C' and (resid 89 through 165 )
12X-RAY DIFFRACTION12chain 'C' and (resid 166 through 180 )
13X-RAY DIFFRACTION13chain 'C' and (resid 181 through 202 )
14X-RAY DIFFRACTION14chain 'C' and (resid 203 through 226 )
15X-RAY DIFFRACTION15chain 'C' and (resid 227 through 243 )
16X-RAY DIFFRACTION16chain 'C' and (resid 244 through 263 )
17X-RAY DIFFRACTION17chain 'D' and (resid 3 through 69 )
18X-RAY DIFFRACTION18chain 'D' and (resid 70 through 88 )
19X-RAY DIFFRACTION19chain 'D' and (resid 89 through 142 )
20X-RAY DIFFRACTION20chain 'D' and (resid 143 through 262 )
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 51 )
22X-RAY DIFFRACTION22chain 'E' and (resid 52 through 69 )
23X-RAY DIFFRACTION23chain 'E' and (resid 70 through 88 )
24X-RAY DIFFRACTION24chain 'E' and (resid 89 through 142 )
25X-RAY DIFFRACTION25chain 'E' and (resid 143 through 202 )
26X-RAY DIFFRACTION26chain 'E' and (resid 203 through 263 )
27X-RAY DIFFRACTION27chain 'F' and (resid 4 through 65 )
28X-RAY DIFFRACTION28chain 'F' and (resid 66 through 85 )
29X-RAY DIFFRACTION29chain 'F' and (resid 86 through 129 )
30X-RAY DIFFRACTION30chain 'F' and (resid 130 through 261 )

+
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