[English] 日本語
Yorodumi
- PDB-4dfu: Inhibition of an antibiotic resistance enzyme: crystal structure ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dfu
TitleInhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA in complex with kanamycin inhibited with quercetin
ComponentsAPH(2")-Id
KeywordsTRANSFERASE/ANTIBOTIC/INHIBITOR / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / TRANSFERASE-ANTIBIOTIC-INHIBITOR COMPLEX / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / KINASE / TRANSFERASE / AMINOGLYCOSIDES / KANAMYCIN / FLAVANOIDS / QUERCETIN / INTRACELLULAR / ANTIBOTIC / TRANSFERASE-ANTIBOTIC-INHIBITOR complex
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
KANAMYCIN A / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsStogios, P.J. / Minasov, G. / Dong, A. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Li, H. / Shakya, T. / Wright, G.D. / Savchenko, A. ...Stogios, P.J. / Minasov, G. / Dong, A. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Li, H. / Shakya, T. / Wright, G.D. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Chem.Biol. / Year: 2011
Title: A small molecule discrimination map of the antibiotic resistance kinome.
Authors: Shakya, T. / Stogios, P.J. / Waglechner, N. / Evdokimova, E. / Ejim, L. / Blanchard, J.E. / McArthur, A.G. / Savchenko, A. / Wright, G.D.
History
DepositionJan 24, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2012ID: 3VCQ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APH(2")-Id
B: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5059
Polymers76,5582
Non-polymers1,9477
Water3,027168
1
A: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1014
Polymers38,2791
Non-polymers8223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2")-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4035
Polymers38,2791
Non-polymers1,1244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.141, 101.814, 70.249
Angle α, β, γ (deg.)90.00, 96.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein APH(2")-Id / APH(2")-IVA


Mass: 38279.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: APH(2")-Id / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68183
#2: Chemical ChemComp-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H10O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NACL, 0.1 M HEPES PH 7.5, 29% PEG3350, 1 MM KANAMYCIN, 5 MM QUERCITIN, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 25, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 81833 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.041 / Net I/σ(I): 37.31
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.704 / Rsym value: 0.592 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DBX

4dbx


Resolution: 1.98→19.837 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.07 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 3879 4.75 %random
Rwork0.2194 ---
obs0.2219 81608 98.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.378 Å2-0 Å2-3.3707 Å2
2---32.4349 Å2-0 Å2
3----20.449 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 134 168 5211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085233
X-RAY DIFFRACTIONf_angle_d1.2477086
X-RAY DIFFRACTIONf_dihedral_angle_d14.6082007
X-RAY DIFFRACTIONf_chiral_restr0.069752
X-RAY DIFFRACTIONf_plane_restr0.008898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.05070.34373780.33447712X-RAY DIFFRACTION97
2.0507-2.13270.31913850.30547691X-RAY DIFFRACTION98
2.1327-2.22970.34083770.28387730X-RAY DIFFRACTION98
2.2297-2.3470.35533900.26797794X-RAY DIFFRACTION99
2.347-2.49380.34633940.2567793X-RAY DIFFRACTION99
2.4938-2.68590.30113950.24647900X-RAY DIFFRACTION100
2.6859-2.95540.32323870.25317769X-RAY DIFFRACTION100
2.9554-3.38130.29493910.22747845X-RAY DIFFRACTION99
3.3813-4.25310.21163870.18487794X-RAY DIFFRACTION99
4.2531-19.8380.23043950.18077701X-RAY DIFFRACTION98
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)
12.54930.06040.54482.60860.23871.797-0.052-0.06690.04110.0863-0.01450.0442-0.15740.015900.24720.0008-0.01610.3189-0.01190.2879-9.654622.6515-22.5487
22.3319-0.45030.47212.46990.0231.68130.11950.21380.0131-0.0815-0.09640.16410.2854-0.0864-00.501-0.03330.0340.5184-0.0290.4407-12.8118-10.2929-15.5213
31.04181.50410.3943.55471.17361.06710.04030.1434-0.0528-0.23770.0418-0.32040.07540.1542-00.54880.0240.0140.6580.03960.60213.13527.8556-38.2194
40.6304-0.6590.06962.4807-0.620.54150.0569-0.03840.04440.2254-0.0402-0.2719-0.09320.055700.6387-0.05430.01370.5507-0.00550.53-1.63942.56342.7746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 3:99
2X-RAY DIFFRACTION2chain B and resid 3:99
3X-RAY DIFFRACTION3chain A and resid 100:298
4X-RAY DIFFRACTION4chain B and resid 100:299

+
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