[English] 日本語
Yorodumi
- PDB-2bkk: Crystal structure of Aminoglycoside Phosphotransferase APH(3')-II... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bkk
TitleCrystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a
Components
  • AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
  • DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-DESIGNED PROTEIN COMPLEX / ANKYRIN REPEAT / CO-CRYSTALLIZATION / INHIBITOR DESIGN / DRUG DESIGN / ENZYME INHIBITION / KINASE INHIBITION / DESIGNED REPEAT PROTEIN / ANTIBIOTIC RESISTANCE / ATP-BINDING / KINASE / PLASMID / TRANSFERASE / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP binding
Similarity search - Function
Aminoglycoside 3-phosphotransferase / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Phosphorylase Kinase; domain 1 ...Aminoglycoside 3-phosphotransferase / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Aminoglycoside 3'-phosphotransferase / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKohl, A. / Amstutz, P. / Parizek, P. / Binz, H.K. / Briand, C. / Capitani, G. / Forrer, P. / Pluckthun, A. / Grutter, M.G.
CitationJournal: Structure / Year: 2005
Title: Allosteric Inhibition of Aminoglycoside Phosphotransferase by a Designed Ankyrin Repeat Protein
Authors: Kohl, A. / Amstutz, P. / Parizek, P. / Binz, H.K. / Briand, C. / Capitani, G. / Forrer, P. / Pluckthun, A. / Grutter, M.G.
History
DepositionFeb 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
B: DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
C: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
D: DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,11710
Polymers99,1664
Non-polymers9526
Water6,251347
1
A: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
B: DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0595
Polymers49,5832
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
D: DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0595
Polymers49,5832
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.670, 98.082, 81.300
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE / APH IIIA / KANAMYCIN KINASE TYPE III / NEOMYCIN-KANAMYCIN PHOSPHOTRANSFERASE TYPE III / APH(3')III


Mass: 30979.916 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Description: STREPTOCOCCUS FAECALIS, STAPHYLOCOCCUS AUREUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00554, UniProt: P0A3Y5*PLUS, kanamycin kinase
#2: Protein DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A


Mass: 18602.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: RESISTANCE TO AMINOGLYCOSIDES

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 %
Crystal growDetails: 15-20 % PEG 5500, 0.1 M MES PH 5.9-6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 46440 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MJO, 1J7L

1mjo

1j7l


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE TWO INDEPENDENT COMPLEXES AB AND CD IN THE ASYMMETRIC UNIT
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1122 2.4 %RANDOM
Rwork0.199 ---
obs0.2 45310 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å22.37 Å2
2---0.53 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6595 0 58 347 7000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216786
X-RAY DIFFRACTIONr_bond_other_d0.0020.026020
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9819183
X-RAY DIFFRACTIONr_angle_other_deg0.872314075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8775815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027515
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021310
X-RAY DIFFRACTIONr_nbd_refined0.230.21792
X-RAY DIFFRACTIONr_nbd_other0.2370.27481
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.24068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2770.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.74624069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.66936525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.90122717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.90732658
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.386 3
Rwork0.274 2588

+
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