[English] 日本語
Yorodumi
- PDB-5dwm: Crystal structure of Phosphinothricin N-acetyltransferase from Br... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dwm
TitleCrystal structure of Phosphinothricin N-acetyltransferase from Brucella ovis
ComponentsPhosphinothricin N-acetyltransferase
KeywordsTRANSFERASE / SSGCID / Brucella ovis / brucellosis / Phosphinothricin N-acetyltransferase / AcetylCoA / iodide phasing / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
IMIDAZOLE / Phosphinothricin N-acetyltransferase
Similarity search - Component
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Phosphinothricin N-acetyltransferase from Brucella ovis
Authors: Clifton, M.C. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphinothricin N-acetyltransferase
B: Phosphinothricin N-acetyltransferase
C: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,97913
Polymers82,3624
Non-polymers6179
Water18,7721042
1
A: Phosphinothricin N-acetyltransferase
B: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3745
Polymers41,1812
Non-polymers1933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-6 kcal/mol
Surface area15440 Å2
MethodPISA
2
C: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6048
Polymers41,1812
Non-polymers4236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-3 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.110, 61.770, 77.030
Angle α, β, γ (deg.)101.730, 92.290, 115.330
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Phosphinothricin N-acetyltransferase


Mass: 20590.475 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria)
Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: pat, BOV_0087 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3AQB6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.59 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: native data: Molecular dimensions Morpheus screen, F3: 10% w/v PEG 4000, 20% v/v glycerol, 20mM of each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, D-N-acetyld-glucosamine, 100mM ...Details: native data: Molecular dimensions Morpheus screen, F3: 10% w/v PEG 4000, 20% v/v glycerol, 20mM of each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, D-N-acetyld-glucosamine, 100mM MES/imidazole pH 6.5, BrovA.17352.a.B1.PS02313 at 4mg/ml, supplemented with 5mM Mg/AMPPNP, cryo: direct , tray 261581 f3, puck dka9-1, iodide data: crystals from the same well were soaked for 20sec in reservoir with 10% EG and 500mM NaI and then vitrified, tray 261581 f3, puck hml1 6-3, anomalous differences for the iodide data set are provided with the structure

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97856
ROTATING ANODERIGAKU MICROMAX-007 HF21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDMar 18, 2015
RIGAKU SATURN 944+2CCDMar 16, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2Rigaku VariMaxSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
21.54181
ReflectionNumber: 565188 / Rmerge(I) obs: 0.063 / Χ2: 1.34 / D res high: 2 Å / Num. obs: 103744 / % possible obs: 94.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.9450107910.031
6.328.94202110.034
5.166.32270310.039
4.475.16339210.034
44.47385410.034
3.654423010.038
3.383.65460010.042
3.163.38501610.046
2.983.16528310.056
2.832.98555210.065
2.72.83590910.079
2.582.7607010.091
2.482.58642910.106
2.392.48650510.118
2.312.39683410.128
2.242.31710610.149
2.172.24718710.157
2.112.17731810.18
2.052.11678410.198
22.05587210.228
ReflectionResolution: 1.45→50 Å / Num. all: 146403 / Num. obs: 140786 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 15.69 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.055 / Χ2: 1.006 / Net I/σ(I): 20.96 / Num. measured all: 550962
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.490.8510.4753.234052010822102010.54994.3
1.49-1.530.8920.3974.01395141053299480.45994.5
1.53-1.570.9210.3374.84388171031497670.3994.7
1.57-1.620.9430.2756.0537643995794760.31895.2
1.62-1.670.9610.2257.4536727970492570.2695.4
1.67-1.730.9730.1848.9935240928988830.21395.6
1.73-1.80.9840.14311.4134347904386850.16596
1.8-1.870.990.10914.4332994870283680.12696.2
1.87-1.960.9940.08318.2631623831780400.09696.7
1.96-2.050.9960.06522.3630338799077250.07596.7
2.05-2.160.9970.0527.5928505751873070.05897.2
2.16-2.290.9980.04331.0727139716369580.0597.1
2.29-2.450.9980.03734.5825519674665780.04397.5
2.45-2.650.9980.03337.9223515624260980.03997.7
2.65-2.90.9990.02743.1521521574055940.03297.5
2.9-3.240.9990.02348.6819532522851150.02797.8
3.24-3.740.9990.0254.2416987458144900.02498
3.74-4.590.9990.01857.7414185386537960.02298.2
4.59-6.480.9990.01957.2110939301029450.02397.8
6.48-500.9990.0256.395357164015550.02494.8

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD
Starting model: iodide phased

Resolution: 1.45→26.173 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1728 6917 4.92 %Random selection
Rwork0.1408 133815 --
obs0.1424 140732 96.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.77 Å2 / Biso mean: 21.9414 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 1.45→26.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 48 1051 6577
Biso mean--44.61 34.62 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055913
X-RAY DIFFRACTIONf_angle_d0.7628067
X-RAY DIFFRACTIONf_chiral_restr0.077884
X-RAY DIFFRACTIONf_plane_restr0.0051064
X-RAY DIFFRACTIONf_dihedral_angle_d16.0472223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.2172150.16654366458194
1.4665-1.48370.2072070.16374409461694
1.4837-1.50180.20272010.1564394459594
1.5018-1.52080.21412200.14994380460094
1.5208-1.54080.21022150.14684433464894
1.5408-1.56190.20382430.14394349459295
1.5619-1.58430.18332390.13954393463295
1.5843-1.60790.18422260.13274441466795
1.6079-1.6330.18462390.12994363460295
1.633-1.65980.17592420.12964437467996
1.6598-1.68840.1952440.12754406465095
1.6884-1.71910.17332320.12854430466296
1.7191-1.75220.17512450.13344445469096
1.7522-1.78790.18042400.134423466396
1.7879-1.82680.18322230.12964488471196
1.8268-1.86930.18222330.13234455468896
1.8693-1.9160.17132170.13594479469697
1.916-1.96780.18762300.13924538476897
1.9678-2.02570.15842340.13234465469997
2.0257-2.0910.17482420.13384473471597
2.091-2.16570.16232460.13374476472297
2.1657-2.25240.16992270.1334503473097
2.2524-2.35480.16762390.14014534477397
2.3548-2.47890.16892420.14334519476197
2.4789-2.63410.17182640.15074481474598
2.6341-2.83720.16112400.14714549478997
2.8372-3.12230.17652510.15014507475898
3.1223-3.57320.18722100.14324575478598
3.5732-4.49810.15432080.13554580478898
4.4981-26.17720.15632030.14944524472797

+
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