[English] 日本語
Yorodumi
- PDB-7d5q: Structure of NorC transporter (K398A mutant) in an outward-open c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d5q
TitleStructure of NorC transporter (K398A mutant) in an outward-open conformation in complex with a single-chain Indian camelid antibody
Components
  • Drug transporter, putative
  • ICab
KeywordsMEMBRANE PROTEIN / NorC / major facilitator superfamily / transporter / outward-open
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / transmembrane transporter activity / plasma membrane / Drug transporter, putative
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsKumar, S. / Athreya, A. / Penmatsa, A.
Funding support India, 2items
OrganizationGrant numberCountry
Wellcome TrustIA/1/15/2/502063 India
Department of Biotechnology (DBT, India)BT/PR31976/MED/29/1421/2019 India
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis of inhibition of a transporter from Staphylococcus aureus, NorC, through a single-domain camelid antibody.
Authors: Kumar, S. / Athreya, A. / Gulati, A. / Nair, R.M. / Mahendran, I. / Ranjan, R. / Penmatsa, A.
History
DepositionSep 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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: Drug transporter, putative
B: Drug transporter, putative
C: ICab
D: ICab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3576
Polymers130,2264
Non-polymers1312
Water0
1
A: Drug transporter, putative
C: ICab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1783
Polymers65,1132
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-22 kcal/mol
Surface area20820 Å2
MethodPISA
2
B: Drug transporter, putative
D: ICab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1783
Polymers65,1132
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-21 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.071, 139.148, 115.555
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPROAA11 - 45211 - 452
21LEULEUPROPROBB11 - 45211 - 452
12GLNGLNSERSERCC5 - 1351 - 131
22GLNGLNSERSERDD5 - 1351 - 131

NCS ensembles :
ID
1
2

-
Components

#1: Protein Drug transporter, putative


Mass: 50855.195 Da / Num. of mol.: 2 / Mutation: K398A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: SACOL0086 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0A0H2WZS4
#2: Protein ICab


Mass: 14257.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 74.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M HEPES pH 6.0, 50 mM NaCl, 57.1 mM CaCl2, 35.7% PEG600, 10 mM YCl3, 6.66 mM CHAPSO

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.6→139.15 Å / Num. obs: 24925 / % possible obs: 99.9 % / Redundancy: 17.1 % / Biso Wilson estimate: 155.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.043 / Net I/σ(I): 8.5
Reflection shellResolution: 3.6→3.84 Å / Redundancy: 10.1 % / Rmerge(I) obs: 2.76 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4460 / CC1/2: 0.486 / Rpim(I) all: 0.88 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D5P

7d5p


Resolution: 3.6→111.52 Å / Cor.coef. Fo:Fc: 0.795 / Cor.coef. Fo:Fc free: 0.92 / SU B: 50.589 / SU ML: 0.705 / Cross valid method: THROUGHOUT / ESU R Free: 0.649 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31463 1231 5 %RANDOM
Rwork0.30767 ---
obs0.30802 23584 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 154.525 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å2-0 Å2-8.63 Å2
2--2.25 Å2-0 Å2
3---4.85 Å2
Refinement stepCycle: 1 / Resolution: 3.6→111.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7487 0 2 0 7489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137620
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177122
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.60910401
X-RAY DIFFRACTIONr_angle_other_deg1.0921.55516275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01851064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86722.118203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.159151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2351514
X-RAY DIFFRACTIONr_chiral_restr0.0320.21107
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021585
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.29917.5264292
X-RAY DIFFRACTIONr_mcbond_other4.2917.5264291
X-RAY DIFFRACTIONr_mcangle_it7.29426.2815344
X-RAY DIFFRACTIONr_mcangle_other7.29426.2815345
X-RAY DIFFRACTIONr_scbond_it3.42717.4873328
X-RAY DIFFRACTIONr_scbond_other3.42517.4873328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.09426.1985058
X-RAY DIFFRACTIONr_long_range_B_refined11.0368955
X-RAY DIFFRACTIONr_long_range_B_other11.0388955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A119040.06
12B119040.06
21C37940.05
22D37940.05
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 75 -
Rwork0.401 1763 -
obs--99.62 %

+
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