[English] 日本語
Yorodumi
- PDB-6edd: Crystal structure of a GNAT Superfamily PA3944 acetyltransferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6edd
TitleCrystal structure of a GNAT Superfamily PA3944 acetyltransferase in complex with CoA (P1 space group)
ComponentsAcetyltransferase PA3944
KeywordsTRANSFERASE / PA3944 / GNAT / acetyltransferase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / COENZYME A / Acetyltransferase PA3944
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCzub, M.P. / Porebski, P.J. / Majorek, K.A. / Satchell, K.J. / Joachimiak, A. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Biochemistry / Year: 2018
Title: A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro.
Authors: Czub, M.P. / Zhang, B. / Chiarelli, M.P. / Majorek, K.A. / Joe, L. / Porebski, P.J. / Revilla, A. / Wu, W. / Becker, D.P. / Minor, W. / Kuhn, M.L.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyltransferase PA3944
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,15815
Polymers44,1922
Non-polymers1,96613
Water8,485471
1
A: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9887
Polymers22,0961
Non-polymers8926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyltransferase PA3944
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1708
Polymers22,0961
Non-polymers1,0747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.452, 44.175, 60.125
Angle α, β, γ (deg.)81.880, 73.320, 89.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 9 - 191 / Label seq-ID: 11 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Acetyltransferase PA3944 / GCN5-related N-acetyltransferase / GNAT


Mass: 22096.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA3944 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q9HX72, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Non-polymers , 5 types, 484 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 ul of 10 mg/ml protein incubated with 5mM CoA and 5 mM colistin was mixed with 0.2 ul of the well condition (MCSG suite I condition 11 - 100 mM Tris-HCl pH 7.0, 200 mM calcium acetate, ...Details: 0.3 ul of 10 mg/ml protein incubated with 5mM CoA and 5 mM colistin was mixed with 0.2 ul of the well condition (MCSG suite I condition 11 - 100 mM Tris-HCl pH 7.0, 200 mM calcium acetate, 20% w/v PEG 3000) and equilibrated against well solution in 96 Well 3 drop Crystallization Plate (Swissci).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.914
11H, -K, H-L20.086
ReflectionResolution: 1.55→50 Å / Num. obs: 49684 / % possible obs: 96.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.044 / Rrim(I) all: 0.069 / Χ2: 1.423 / Net I/σ(I): 11.7 / Num. measured all: 121370
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.582.10.39724400.7730.3350.5210.7993.5
1.58-1.612.40.3823830.7760.3210.50.85694.1
1.61-1.642.50.31625160.8290.2660.4140.83795.1
1.64-1.672.50.29224200.8540.2460.3830.87195.2
1.67-1.712.50.23524700.8950.1980.3090.90395.4
1.71-1.752.50.21324850.9040.1780.2790.93395.9
1.75-1.792.50.17824610.9340.1490.2330.98895.6
1.79-1.842.50.15125070.9540.1260.1971.02396
1.84-1.892.50.12624320.9640.1050.1651.12696
1.89-1.952.50.11224910.970.0940.1471.45396
1.95-2.022.50.08525200.9820.0710.1121.39996.7
2.02-2.12.50.07324800.9880.060.0951.45796.9
2.1-2.22.50.06424960.990.0530.0831.61397.2
2.2-2.322.50.05925400.9910.0490.0771.77297.4
2.32-2.462.50.05225130.9930.0420.0671.68497.6
2.46-2.652.50.04725250.9940.0380.0611.80397.8
2.65-2.922.50.04325050.9940.0350.0562.03897.7
2.92-3.342.40.03625550.9950.0290.0472.15297.7
3.34-4.212.40.03124600.9970.0250.042.09696.4
4.21-502.40.03424850.9960.0270.0442.50195.7

-
Processing

Software
NameClassification
HKL-3000data reduction
HKL-3000data scaling
SCALEPACKdata scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDV

6edv


Resolution: 1.55→34.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.0202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.019
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2225 4.7 %RANDOM
Rwork0.1656 ---
obs0.167 44683 91.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 19.859 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-11.34 Å25.97 Å22.72 Å2
2---15.22 Å2-1.77 Å2
3---3.88 Å2
Refinement stepCycle: final / Resolution: 1.55→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 130 476 3642
Biso mean--22.9 31.34 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0143360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172859
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6814599
X-RAY DIFFRACTIONr_angle_other_deg1.7311.6716717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.94619.144222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06215491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.491546
X-RAY DIFFRACTIONr_chiral_restr0.0810.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023977
X-RAY DIFFRACTIONr_gen_planes_other0.010.02675
Refine LS restraints NCS

Ens-ID: 1 / Number: 6260 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.554→1.594 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 53 -
Rwork0.201 1129 -
all-1182 -
obs--30.76 %
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)
14.18180.480.15813.1643-2.18773.9929-0.38780.2381-0.3513-0.17970.0087-0.53810.67840.6490.3790.22390.07870.05070.26140.01610.162525.706-2.94961.185
22.201-1.90460.24921.9031-0.02140.79040.17110.2893-0.2474-0.1369-0.1970.2760.0936-0.11440.02590.037-0.02860.00450.2201-0.00520.143912.978-1.87451.205
31.9927-0.8683-1.04670.38330.50342.69270.2130.3385-0.1885-0.1163-0.14880.0786-0.0998-0.0981-0.06430.18070.0054-0.00670.2895-0.0090.18979.1785.99644.816
42.32131.1101-1.2012.8719-0.39371.8458-0.02050.1206-0.0234-0.1166-0.0013-0.10590.11920.10580.02180.01910.00220.00530.12730.00190.069521.7450.42752.936
51.17620.8478-0.57352.2152-0.02030.96080.03170.0448-0.0377-0.00790.0037-0.106-0.01120.0625-0.03530.0041-0.0040.01040.12390.00450.075421.51110.35259.015
61.20660.72460.1553.3912-0.09561.57650.0523-0.00130.02870.0583-0.03970.1498-0.1378-0.133-0.01250.0240.00240.02260.10360.00350.061412.16218.75962.539
71.6406-0.29581.60871.8405-0.43615.7229-0.02760.20150.0691-0.1885-0.0040.1616-0.1467-0.21290.03150.0608-0.00450.02790.12920.00520.091112.92122.25151.329
85.81222.96574.63416.62617.424511.15490.2594-0.87350.32920.6791-0.36110.57580.1437-0.7060.10170.2535-00.14580.27460.02820.283725.75216.25370.961
95.9849-1.7876-4.34357.57463.38936.7624-0.1220.29870.0557-0.4109-0.0432-0.077-0.01840.15530.16520.266-0.0020.00170.34440.03410.263713.56211.27341.24
101.55460.99780.86151.63220.01143.97940.0822-0.16-0.12740.0672-0.00350.16720.3123-0.2828-0.07860.04640.00610.01430.13010.01420.105720.4899.38126.732
113.0860.1471-0.49540.446-0.20061.06510.004-0.13550.09490.1264-0.0138-0.0758-0.04370.12940.00990.0473-0.01430.00240.1690.00960.099627.17718.43434.228
121.1544-0.3158-0.52792.2486-0.97931.6790.0244-0.1030.07110.21060.0126-0.0327-0.08960.0248-0.0370.0256-0.01890.00220.12760.00110.056223.11420.16526.002
138.8076-4.5022-1.94523.04040.94641.2631-0.02080.1896-0.1593-0.06-0.01230.27460.0405-0.22220.0330.0768-0.0106-0.00850.10620.01520.080116.74320.01817.235
142.1674-0.7479-0.22643.8478-0.4341.428-0.0016-0.26630.08870.3990.0108-0.2248-0.2120.1067-0.00920.071-0.02110.00370.1250.01150.08227.833.19223.97
155.28371.26412.50265.2111.57536.16560.0213-0.40320.10710.45670.0012-0.3743-0.04560.1176-0.02260.11050.00860.0180.10710.01080.114326.05435.45924.836
162.2792-3.01875.35636.1327-6.770512.65330.17920.41020.119-0.827-0.381-0.40610.31310.92930.20170.19960.05840.11050.35710.08620.244315.10929.62911.007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 17
2X-RAY DIFFRACTION2A18 - 42
3X-RAY DIFFRACTION3A43 - 56
4X-RAY DIFFRACTION4A57 - 85
5X-RAY DIFFRACTION5A86 - 140
6X-RAY DIFFRACTION6A141 - 164
7X-RAY DIFFRACTION7A165 - 185
8X-RAY DIFFRACTION8A186 - 192
9X-RAY DIFFRACTION9B0 - 8
10X-RAY DIFFRACTION10B9 - 32
11X-RAY DIFFRACTION11B33 - 69
12X-RAY DIFFRACTION12B70 - 112
13X-RAY DIFFRACTION13B113 - 134
14X-RAY DIFFRACTION14B135 - 175
15X-RAY DIFFRACTION15B176 - 185
16X-RAY DIFFRACTION16B186 - 192

+
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