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- PDB-7d5p: Structure of NorC transporter in an outward-open conformation in ... -

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Basic information

Entry
Database: PDB / ID: 7d5p
TitleStructure of NorC transporter 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 / homology
Function and homology information


transmembrane transporter activity / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Quinolone resistance protein NorB
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.65 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 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Drug transporter, putative
B: Drug transporter, putative
C: ICab
D: ICab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0676
Polymers131,9364
Non-polymers1312
Water00
1
A: Drug transporter, putative
C: ICab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0343
Polymers65,9682
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-20 kcal/mol
Surface area20920 Å2
MethodPISA
2
B: Drug transporter, putative
D: ICab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0343
Polymers65,9682
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-23 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.212, 139.875, 118.034
Angle α, β, γ (deg.)90.00, 106.03, 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: _ / Refine code: _

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

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Components

#1: Protein Drug transporter, putative


Mass: 51710.504 Da / Num. of mol.: 2
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
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M HEPES, pH 6.0, 50 mM NaCl, 35.7% PEG 600, 57.1 mM CaCl2, 10 mM YtCl2, 6.66 mM CHAPSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.65→49.18 Å / Num. obs: 24592 / % possible obs: 99.1 % / Redundancy: 17.5 % / Biso Wilson estimate: 141.41 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.048 / Net I/σ(I): 8
Reflection shellResolution: 3.65→3.9 Å / Redundancy: 16.1 % / Rmerge(I) obs: 4.14 / Mean I/σ(I) obs: 1 / Num. unique obs: 4248 / CC1/2: 0.563 / Rpim(I) all: 1.05 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
ADDREFdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.65→48.96 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.892 / SU B: 54.517 / SU ML: 0.738 / Cross valid method: THROUGHOUT / ESU R Free: 0.672 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31763 1153 4.7 %RANDOM
Rwork0.29746 ---
obs0.29839 23409 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.168 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å2-0 Å2-12.5 Å2
2--4.91 Å20 Å2
3---4.24 Å2
Refinement stepCycle: 1 / Resolution: 3.65→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7573 0 2 0 7575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177243
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.61610518
X-RAY DIFFRACTIONr_angle_other_deg1.0591.55516556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24751071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67722.087206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88415991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9811514
X-RAY DIFFRACTIONr_chiral_restr0.0330.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021606
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_it3.99416.1964320
X-RAY DIFFRACTIONr_mcbond_other3.9916.1964319
X-RAY DIFFRACTIONr_mcangle_it6.87724.2815379
X-RAY DIFFRACTIONr_mcangle_other6.87624.2815380
X-RAY DIFFRACTIONr_scbond_it3.22716.2123389
X-RAY DIFFRACTIONr_scbond_other3.22316.2123389
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.76224.2775140
X-RAY DIFFRACTIONr_long_range_B_refined11.2738995
X-RAY DIFFRACTIONr_long_range_B_other11.2738995
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)
11A120280.07
12B120280.07
21C38030.04
22D38030.04
LS refinement shellResolution: 3.651→3.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 63 -
Rwork0.422 1580 -
obs--89.15 %

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