[English] 日本語
Yorodumi
- PDB-4my3: Crystal Structure of GCN5-related N-acetyltransferase from Kribbe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4my3
TitleCrystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta structure
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsKim, Y. / Mack, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida
Authors: Kim, Y. / Mack, J. / Endres, M. / Joachimiak, A.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
E: GCN5-related N-acetyltransferase
F: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,35610
Polymers255,1616
Non-polymers1954
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22060 Å2
ΔGint-75 kcal/mol
Surface area87340 Å2
MethodPISA
2
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1254
Polymers85,0542
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-34 kcal/mol
Surface area32320 Å2
MethodPISA
3
C: GCN5-related N-acetyltransferase
D: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1784
Polymers85,0542
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-7 kcal/mol
Surface area31840 Å2
MethodPISA
4
E: GCN5-related N-acetyltransferase
F: GCN5-related N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)85,0542
Polymers85,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-18 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.246, 167.120, 183.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailshexamer as in the asymmetric unit

-
Components

#1: Protein
GCN5-related N-acetyltransferase


Mass: 42526.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_4406 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D2PVF8
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR STATES THAT THE N-TERMINAL SER ASN ALA ARE CLONING ARTIFACTS THAT ARE RESIDUAL OF THE ...THE AUTHOR STATES THAT THE N-TERMINAL SER ASN ALA ARE CLONING ARTIFACTS THAT ARE RESIDUAL OF THE CLEAVED HIS-TAG AND VAL IS AN EXPRESSION ARTIFACT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M MES pH 6.5, 10 %(w/v) PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. all: 90603 / Num. obs: 90603 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 39.98 Å2 / Rsym value: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4461 / Rsym value: 0.792 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.57→41.966 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4161 5.04 %random
Rwork0.176 ---
obs0.179 82586 93.96 %-
all-82586 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 2.57→41.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17709 0 10 401 18120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818215
X-RAY DIFFRACTIONf_angle_d1.18424792
X-RAY DIFFRACTIONf_dihedral_angle_d16.1516434
X-RAY DIFFRACTIONf_chiral_restr0.0782696
X-RAY DIFFRACTIONf_plane_restr0.0053280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.57-2.59920.365790.24181485156454
2.5992-2.62980.3493940.24191714180862
2.6298-2.66180.31411070.2452004211173
2.6618-2.69550.33491300.24342253238082
2.6955-2.7310.3381280.24382479260791
2.731-2.76840.30771470.22812621276896
2.7684-2.80790.33831260.23622696282297
2.8079-2.84980.31421510.2282685283698
2.8498-2.89440.27911410.22632720286198
2.8944-2.94180.27921510.22482718286999
2.9418-2.99250.34631400.23352737287799
2.9925-3.04690.29251460.22152700284699
3.0469-3.10550.26431470.20962716286398
3.1055-3.16890.27361420.20262709285198
3.1689-3.23780.27641430.20672688283198
3.2378-3.3130.2461400.20642739287998
3.313-3.39590.26791230.2022762288599
3.3959-3.48760.30171390.2012697283699
3.4876-3.59020.25151570.18832752290999
3.5902-3.7060.21741500.17272750290099
3.706-3.83840.21311620.16422693285599
3.8384-3.9920.22671650.14982736290199
3.992-4.17350.19381490.14272750289999
4.1735-4.39330.18211370.13372778291599
4.3933-4.66820.18191510.12812760291199
4.6682-5.02810.18541490.13162766291599
5.0281-5.53310.191240.14662828295299
5.5331-6.33140.2271360.16542796293298
6.3314-7.9680.19851630.16012813297698
7.968-41.97140.16541440.14532880302496
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)
12.3099-0.82341.48892.85051.01293.22830.13790.7872-0.0785-0.09710.057-0.71710.23720.6657-0.14260.37860.15780.05540.577-0.02620.451748.7077-9.3495-14.3105
20.78780.4823-0.09842.1198-0.23161.32080.1960.0237-0.10460.3563-0.0994-0.2460.12640.2973-0.05050.22650.0122-0.01230.2803-0.00310.186244.02446.071-9.35
32.3683-0.4663-0.60022.4702-0.51412.90880.1271-0.00640.0256-0.1114-0.2289-0.33150.17980.60230.09840.2033-0.03630.03930.410.0490.254453.283420.8354-20.0005
40.7617-0.71790.54841.2844-1.2572.229-0.1546-0.13090.13270.27270.0802-0.1134-0.2416-0.02960.05730.3243-0.064-0.01070.2354-0.01480.176735.702918.20822.7158
50.6810.0901-0.63922.3155-0.89933.1178-0.050.04520.11270.036-0.13080.3268-0.0866-0.60970.09810.1277-0.01370.04020.2587-0.09730.322723.265846.5458-29.7455
63.93552.2024-0.73552.75190.1141.34230.1926-0.18670.40.1975-0.2290.5119-0.1862-0.26940.03220.2847-0.03760.05880.2656-0.06030.257214.223323.6951-12.9897
70.73020.0965-0.29461.6861-0.16080.08560.0653-0.20710.06180.396-0.0798-0.12550.02230.05330.01410.3273-0.0811-0.02750.294-0.01080.159935.543237.1665-10.4322
81.4109-0.72331.02692.3143-0.68872.8769-0.0964-0.11170.09380.0838-0.008-0.6253-0.09480.35410.09270.14350.01230.05740.3343-0.00170.440964.010917.2969-48.2054
91.29851.0711-0.23524.56670.91541.0882-0.0647-0.1665-0.4486-0.143-0.0899-0.58920.1160.16370.12510.27440.08130.00910.19730.04970.327945.21041.0318-63.9806
101.70220.71280.39742.09780.45651.4656-0.2010.02380.2648-0.87470.0067-0.2556-0.54650.2540.13250.69560.04810.01660.20330.04130.315753.148328.807-67.7934
111.79650.8713-0.70282.1279-0.57951.5725-0.0677-0.04820.47950.32150.14040.5228-0.4013-0.609-0.01120.25910.1733-0.05770.4092-0.04760.32515.862420.6252-65.6182
120.63071.0024-0.05161.280.40060.3618-0.1070.06590.0749-0.16860.11570.0612-0.0456-0.04530.00420.24810.0608-0.08430.1727-0.00760.185422.608724.091-66.1636
131.69260.51920.06782.26031.71873.29950.07620.00570.0831-0.1218-0.23180.2556-0.2549-0.29410.10820.19590.043-0.02410.1673-0.03770.243128.669934.8943-55.1899
140.82240.30860.76781.36771.09262.9733-0.09520.12460.0448-0.28210.0601-0.0561-0.19990.13650.02920.25270.04690.00630.1557-0.00250.173633.516518.9552-78.2423
153.4876-0.9246-0.95071.1539-0.32141.4491-0.1135-0.0965-0.0506-0.0002-0.0236-0.1633-0.0344-0.02720.12480.22680.0483-0.0140.1167-0.04050.195636.8059-25.2111-52.3428
160.575-0.04270.8231.61921.00583.82440.03860.0386-0.04430.54160.0459-0.28390.42440.1877-0.05180.33920.0664-0.01590.1993-0.01380.193225.8558-18.2902-27.3186
172.6042-0.62820.31861.9429-0.79861.7486-0.0902-0.1709-0.62040.08230.23570.74830.3347-0.4299-0.04590.1593-0.0274-0.01010.3448-0.01880.42510.7796-32.4182-51.0133
183.83880.7364-1.23253.2613-3.23617.202-0.0667-0.33630.3640.2107-0.48480.1656-0.840.3630.36750.32840.0745-0.00390.4804-0.18390.4344-5.319513.4317-21.6912
191.611-0.43050.33632.42370.78682.00070.0335-0.20810.10270.1922-0.36750.44870.039-0.2960.28350.1616-0.04340.05960.4494-0.09130.3488-5.37610.8945-24.7176
20-0.02150.0917-0.12510.8049-0.34381.83980.11360.11380.1858-0.0811-0.12210.1848-0.1013-0.32380.0050.13250.0775-0.03210.3979-0.06130.23060.0521-5.6044-48.9918
212.8448-0.8004-0.6643.280.19622.21750.08470.12070.4059-0.0445-0.1341-0.0287-0.0397-0.07850.02640.15360.09670.0070.3444-0.02440.13053.7274-1.8697-53.9697
221.5206-0.52580.61081.76240.48910.55540.02950.21230.2005-0.231-0.0404-0.13350.05920.19920.00150.14520.08130.04730.27420.00920.187615.295-6.4208-50.1333
232.4137-0.1887-0.39842.8305-0.61912.27980.0174-0.3486-0.56250.35330.06870.75370.5745-0.5285-0.05040.3927-0.11230.06620.44690.04350.5112-4.9814-22.671-24.7117
242.8951-0.96040.66322.1786-0.1991.3136-0.1201-0.4591-0.45780.45630.16420.0170.5265-0.1352-0.05430.394-0.020.02130.2220.0820.27624.6197-21.36-22.948
251.92890.41810.50820.1746-0.38393.01770.34010.0326-0.47210.293-0.03710.40940.534-0.1239-0.2890.4224-0.0402-0.01790.2908-0.09280.43183.8344-20.9321-30.0412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 263 )
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 389 )
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 131 )
6X-RAY DIFFRACTION6chain 'B' and (resid 132 through 243 )
7X-RAY DIFFRACTION7chain 'B' and (resid 244 through 389 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 131 )
9X-RAY DIFFRACTION9chain 'C' and (resid 132 through 263 )
10X-RAY DIFFRACTION10chain 'C' and (resid 264 through 389 )
11X-RAY DIFFRACTION11chain 'D' and (resid 4 through 72 )
12X-RAY DIFFRACTION12chain 'D' and (resid 73 through 178 )
13X-RAY DIFFRACTION13chain 'D' and (resid 179 through 258 )
14X-RAY DIFFRACTION14chain 'D' and (resid 259 through 389 )
15X-RAY DIFFRACTION15chain 'E' and (resid 4 through 131 )
16X-RAY DIFFRACTION16chain 'E' and (resid 132 through 281 )
17X-RAY DIFFRACTION17chain 'E' and (resid 282 through 389 )
18X-RAY DIFFRACTION18chain 'F' and (resid 4 through 30 )
19X-RAY DIFFRACTION19chain 'F' and (resid 31 through 131 )
20X-RAY DIFFRACTION20chain 'F' and (resid 132 through 197 )
21X-RAY DIFFRACTION21chain 'F' and (resid 198 through 242 )
22X-RAY DIFFRACTION22chain 'F' and (resid 243 through 272 )
23X-RAY DIFFRACTION23chain 'F' and (resid 273 through 337 )
24X-RAY DIFFRACTION24chain 'F' and (resid 338 through 360 )
25X-RAY DIFFRACTION25chain 'F' and (resid 361 through 389 )

+
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