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- PDB-2qfi: Structure of the zinc transporter YiiP -

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Basic information

Entry
Database: PDB / ID: 2qfi
TitleStructure of the zinc transporter YiiP
ComponentsFerrous-iron efflux pump fieF
KeywordsTRANSPORT PROTEIN / zinc transporter
Function / homology
Function and homology information


zinc efflux antiporter activity / zinc:proton antiporter activity / cadmium ion transmembrane transport / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / iron ion transmembrane transport / zinc ion transmembrane transport / intracellular zinc ion homeostasis / intracellular iron ion homeostasis / metal ion binding ...zinc efflux antiporter activity / zinc:proton antiporter activity / cadmium ion transmembrane transport / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / iron ion transmembrane transport / zinc ion transmembrane transport / intracellular zinc ion homeostasis / intracellular iron ion homeostasis / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Cation efflux pump FieF / Alpha-lytic protease prodomain-like / Cation efflux protein transmembrane domain / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily ...Cation efflux pump FieF / Alpha-lytic protease prodomain-like / Cation efflux protein transmembrane domain / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cation-efflux pump FieF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.8 Å
AuthorsLu, M.
CitationJournal: Science / Year: 2007
Title: Structure of the zinc transporter YiiP.
Authors: Lu, M. / Fu, D.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_site
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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrous-iron efflux pump fieF
B: Ferrous-iron efflux pump fieF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3729
Polymers65,9142
Non-polymers4587
Water00
1
A: Ferrous-iron efflux pump fieF
hetero molecules

A: Ferrous-iron efflux pump fieF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,43810
Polymers65,9142
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4270 Å2
ΔGint-254 kcal/mol
Surface area30280 Å2
MethodPISA, PQS
2
B: Ferrous-iron efflux pump fieF
hetero molecules

B: Ferrous-iron efflux pump fieF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3078
Polymers65,9142
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3960 Å2
ΔGint-180 kcal/mol
Surface area30290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.660, 110.839, 130.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 5 - 290 / Label seq-ID: 5 - 290

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ferrous-iron efflux pump fieF


Mass: 32957.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fieF / Plasmid: pET15b / Cell line (production host): BL21/DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P69380
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 5.856 Å3/Da / Density % sol: 78.998 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. all: 16000 / Num. obs: 15534 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 13.3
Reflection shellResolution: 3.8→4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1000 / Rsym value: 0.429 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3.8→12 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.904 / SU B: 71.277 / SU ML: 0.628 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.703
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32934 775 5.1 %RANDOM
Rwork0.32223 ---
obs0.32259 14484 100 %-
all-16000 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.019 Å2
Baniso -1Baniso -2Baniso -3
1-10.48 Å20 Å20 Å2
2--3.47 Å20 Å2
3----13.95 Å2
Refinement stepCycle: LAST / Resolution: 3.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 7 0 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224504
X-RAY DIFFRACTIONr_angle_refined_deg2.8341.9536138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.7215570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.90322.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.53215734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4241532
X-RAY DIFFRACTIONr_chiral_restr0.2140.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023338
X-RAY DIFFRACTIONr_nbd_refined0.3840.23740
X-RAY DIFFRACTIONr_nbtor_refined0.3470.23000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3290.2278
X-RAY DIFFRACTIONr_metal_ion_refined0.2650.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4480.2163
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3980.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4450.23
X-RAY DIFFRACTIONr_mcbond_it1.7941.52976
X-RAY DIFFRACTIONr_mcangle_it3.23624576
X-RAY DIFFRACTIONr_scbond_it1.64331839
X-RAY DIFFRACTIONr_scangle_it2.9244.51562
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2205 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.070.05
tight thermal0.110.5
LS refinement shellResolution: 3.8→3.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 50 -
Rwork0.401 983 -
obs-1000 100 %
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)
15.3839-0.3291-0.65890.29820.75791.9327-0.27430.16530.132-0.07640.10910.46520.30170.48530.1652-0.14140.08540.04050.55830.1535-0.005730.1657-5.219152.5748
20.197-1.59140.685813.9874-3.62255.6410.1707-0.09530.3991.34410.23751.18423.6846-0.5348-0.40813.2421-0.476-0.05370.67050.03620.0263-4.2208-38.623845.7779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2905 - 290
2X-RAY DIFFRACTION2BB5 - 2905 - 290

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