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- PDB-3h90: Structural basis for the autoregulation of the zinc transporter YiiP -

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Basic information

Entry
Database: PDB / ID: 3h90
TitleStructural basis for the autoregulation of the zinc transporter YiiP
ComponentsFerrous-iron efflux pump fieF
KeywordsTRANSPORT PROTEIN / membrane protein / zinc transporter / Cell inner membrane / Cell membrane / Ion transport / Iron / Iron transport / Membrane / Transmembrane / Transport
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 / zinc ion transmembrane transport / iron 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 / zinc ion transmembrane transport / iron 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 / : / Dimerisation domain of Zinc Transporter / 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 / : / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsLu, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural basis for autoregulation of the zinc transporter YiiP.
Authors: Lu, M. / Chai, J. / Fu, D.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,54728
Polymers123,8964
Non-polymers2,65124
Water4,774265
1
A: Ferrous-iron efflux pump fieF
C: Ferrous-iron efflux pump fieF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27314
Polymers61,9482
Non-polymers1,32612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-405 kcal/mol
Surface area30310 Å2
MethodPISA
2
B: Ferrous-iron efflux pump fieF
D: Ferrous-iron efflux pump fieF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27314
Polymers61,9482
Non-polymers1,32612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-402 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.657, 130.704, 115.757
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23B
33D
14C
24B
34D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUARGARG1AA8 - 2151 - 208
211LEULEUARGARG1CC8 - 2151 - 208
121GLNGLNVALVAL1AA216 - 290209 - 283
221GLNGLNVALVAL1CC216 - 290209 - 283
112LEULEULEULEU1BB8 - 1841 - 177
212LEULEULEULEU1DD8 - 1841 - 177
122GLYGLYVALVAL1BB185 - 290178 - 283
222GLYGLYVALVAL1DD185 - 290178 - 283
113LEULEUARGARG4AA8 - 2151 - 208
213LEULEUARGARG4BB8 - 2151 - 208
313LEULEUARGARG4DD8 - 2151 - 208
123GLNGLNVALVAL4AA216 - 290209 - 283
223GLNGLNVALVAL4BB216 - 290209 - 283
323GLNGLNVALVAL4DD216 - 290209 - 283
114LEULEUARGARG4CC8 - 2151 - 208
214LEULEUARGARG4BB8 - 2151 - 208
314LEULEUARGARG4DD8 - 2151 - 208
124GLNGLNVALVAL4CC216 - 290209 - 283
224GLNGLNVALVAL4BB216 - 290209 - 283
324GLNGLNVALVAL4DD216 - 290209 - 283

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Ferrous-iron efflux pump fieF


Mass: 30973.885 Da / Num. of mol.: 4 / Fragment: UNP residues 8-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fieF, yiiP, b3915, JW3886 / Production host: Escherichia coli (E. coli) / References: UniProt: P69380
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity % sol: 80.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: see reference, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511
SYNCHROTRONNSLS X2521
SYNCHROTRONNSLS X2531
SYNCHROTRONNSLS X2541
Detector
IDDetector
1CCD
2CCD
3CCD
4CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 70409 / Num. obs: 65270 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.6
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.4 / % possible all: 54.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.914 / SU B: 30.494 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.465 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27677 3305 5.1 %RANDOM
Rwork0.26127 ---
obs-61831 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.742 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20.99 Å2
2---4.68 Å20 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 24 265 9001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228896
X-RAY DIFFRACTIONr_angle_refined_deg1.451.95412128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16951128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77423.068352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.05151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0051560
X-RAY DIFFRACTIONr_chiral_restr0.1070.21452
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026576
X-RAY DIFFRACTIONr_nbd_refined0.240.24484
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2331
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0070.21
X-RAY DIFFRACTIONr_mcbond_it1.5871.55740
X-RAY DIFFRACTIONr_mcangle_it2.8629068
X-RAY DIFFRACTIONr_scbond_it1.35133582
X-RAY DIFFRACTIONr_scangle_it2.3944.53060
Refine LS restraints NCS

Number: 2178 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Atight positional0.020.05
21Btight positional0.030.05
31Amedium positional0.470.5
32Bmedium positional0.230.5
33Dmedium positional0.240.5
41Cmedium positional0.470.5
42Bmedium positional0.230.5
43Dmedium positional0.240.5
11Atight thermal0.030.5
21Btight thermal0.040.5
31Amedium thermal0.632
32Bmedium thermal0.322
33Dmedium thermal0.322
41Cmedium thermal0.642
42Bmedium thermal0.322
43Dmedium thermal0.322
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 155 -
Rwork0.433 2816 -
obs--59.14 %
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)
128.1861-4.599310.89353.4226-3.23995.01043.23720.6521.2939-1.3214-1.6492-0.18961.1174-0.1103-1.588-0.5666-0.1997-0.6380.0643-0.27650.1419-40.7373-17.064-21.024
25.66440.959-1.72350.9873-0.19960.5347-0.27630.55190.0449-0.2063-0.05550.6347-0.0982-0.10150.3318-0.3654-0.1114-0.2309-0.10850.00270.4133-36.0685-8.4801-10.7195
32.6959-1.95124.8481.4122-3.50888.71811.16590.81590.7758-1.9078-0.7535-0.7894-0.1409-1.051-0.4125-0.1109-0.4940.1487-0.1164-0.07990.2013-60.5189-21.26840.4891
49.74254.8922-0.83693.0283-0.72230.2315-0.14060.2136-0.22930.3121-0.09990.233-0.163-0.1110.2405-0.3695-0.3386-0.1652-0.0904-0.25680.5972-43.6386-25.5621-9.2918
514.65241.9741-0.46660.266-0.06290.0149-0.1398-0.1324-1.67570.323-0.0948-0.67550.7759-0.0160.2346-0.3712-0.21570.1815-0.24490.01890.5193-36.3964-19.48473.749
63.965-0.2068-0.33213.71470.06380.0284-0.2501-0.005-0.19130.15160.4189-0.0299-0.09850.0706-0.1688-0.19990.003-0.0588-0.1427-0.0564-0.0182-1.5696-12.1111-0.1967
75.3986-2.73237.05733.1076-10.136634.213-0.54690.20640.1029-0.0086-0.68220.43560.221-1.09421.22910.02950.0617-0.1491-0.28320.3391-0.6564-5.7078-13.5815-50.1281
80.15970.0964-0.03010.572-1.12842.4048-0.03730.01090.0363-0.23270.3620.2193-0.1598-0.0432-0.32460.27610.03070.052-0.14090.0825-0.306-4.5729-26.8352-45.0279
91.2869-0.17271.5548.90695.82495.97440.36290.73691.2506-1.93110.92392.2523-0.2923-0.4972-1.2868-0.07570.17210.5662-0.4130.09150.032911.4259-26.8736-70.0428
100.50051.2134-1.69393.1849-3.08759.99980.0462-0.2387-0.1649-0.2194-0.3735-0.360.30860.44930.32740.11850.07710.0767-0.14490.1462-0.4966.5884-15.7815-50.6033
111.7755-4.58970.044811.8647-0.11580.0011-0.35210.33520.29180.018-1.2025-2.9138-0.37620.84811.5545-0.195-0.1240.6168-0.0060.0337-0.26321.2768-22.2066-70.458
120.35280.1777-1.33180.4944-0.11665.78680.2006-0.00250.11680.06260.1577-0.20820.0117-0.1095-0.3583-0.07190.07880.0736-0.1632-0.0283-0.04897.7315-30.8412-18.9093
1331.3706-1.3336-7.0712.7706-0.9452.16552.0516-1.7657-0.62080.6186-0.92020.1695-0.6286-0.2374-1.1314-0.74490.23720.60190.1484-0.30490.1852-40.418110.492220.6182
147.7077-4.2281-0.24962.39170.44761.3412-0.0257-0.61760.0365-0.15540.0910.3390.0891-0.1163-0.0653-0.4230.02590.1604-0.1172-0.01540.3441-35.93031.889410.1446
156.57954.9618-0.07473.8260.55964.5078-0.2837-0.3109-0.65682.197-0.4565-0.52041.5504-3.31250.7403-0.2250.6521-0.2054-0.05640.29450.4577-60.314215.0082-0.3198
166.5291-2.68720.91212.7168-1.16060.5102-0.27230.00750.4419-0.34250.17310.12780.1557-0.21920.0992-0.46360.30670.1138-0.1046-0.14450.5189-43.315919.06829.0011
1710.4721-1.1248-0.87380.12080.09390.07290.04320.07351.5609-0.2668-0.1802-0.5887-0.60860.15640.137-0.35140.1802-0.1267-0.2690.14860.5612-36.245612.9658-4.262
184.48791.1112-0.72035.23690.29620.161-0.1164-0.04780.075-0.25050.42810.0610.0230.047-0.3117-0.1691-0.02250.074-0.1367-0.0615-0.0614-1.47635.1992-1.3249
190.0144-0.2076-0.74112.993110.683938.1368-0.9043-0.0738-1.20680.3882-0.62960.24381.23871.66751.53380.15890.13490.3792-0.2335-0.2574-0.60423.6807-63.3431-47.7272
200.22130.08630.29581.65722.23213.1551-0.0460.03930.0486-0.0816-0.0062-0.0942-0.12550.04270.05220.1939-0.03310.0257-0.141-0.0907-0.30982.8034-49.5972-44.0348
2112.067-9.96796.77048.234-5.59273.79870.17221.409-0.1176-0.502-1.71610.07710.59960.18111.54390.0624-0.2132-0.03460.0791-0.1003-0.0179-14.2026-52.1742-67.9056
220.20610.32751.03690.55361.45766.3113-0.0136-0.04630.47240.0675-0.52470.82740.1983-0.15480.53830.0962-0.00150.0482-0.1004-0.2475-0.2537-8.6134-61.0984-47.6769
2328.56318.8558-5.9272.7457-1.83761.2299-0.69441.5456-1.00350.37080.25031.50570.80720.71370.4441-0.0862-0.1743-0.2257-0.0637-0.1925-0.1195-24.0742-56.769-67.2069
240.58690.261.34160.44960.74825.37510.01710.072-0.08450.01490.0560.07960.04070.0295-0.0732-0.08170.0653-0.0403-0.1350.0174-0.0643-8.3651-42.8374-17.8457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 35
2X-RAY DIFFRACTION2A36 - 96
3X-RAY DIFFRACTION3A97 - 117
4X-RAY DIFFRACTION4A118 - 174
5X-RAY DIFFRACTION5A175 - 215
6X-RAY DIFFRACTION6A216 - 290
7X-RAY DIFFRACTION7B8 - 35
8X-RAY DIFFRACTION8B36 - 96
9X-RAY DIFFRACTION9B97 - 117
10X-RAY DIFFRACTION10B118 - 168
11X-RAY DIFFRACTION11B169 - 184
12X-RAY DIFFRACTION12B185 - 290
13X-RAY DIFFRACTION13C8 - 35
14X-RAY DIFFRACTION14C36 - 96
15X-RAY DIFFRACTION15C97 - 117
16X-RAY DIFFRACTION16C118 - 174
17X-RAY DIFFRACTION17C175 - 215
18X-RAY DIFFRACTION18C216 - 290
19X-RAY DIFFRACTION19D8 - 35
20X-RAY DIFFRACTION20D36 - 96
21X-RAY DIFFRACTION21D97 - 117
22X-RAY DIFFRACTION22D118 - 168
23X-RAY DIFFRACTION23D169 - 184
24X-RAY DIFFRACTION24D185 - 290

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