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- PDB-3nwi: The Soluble Domain Structure of the ZntB Zn2+ Efflux System -

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Basic information

Entry
Database: PDB / ID: 3nwi
TitleThe Soluble Domain Structure of the ZntB Zn2+ Efflux System
ComponentsZinc transport protein zntB
KeywordsTRANSPORT PROTEIN / alpha-beta-alpha / zinc efflux transporter / membrane
Function / homology
Function and homology information


zinc ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / cobalt ion binding / magnesium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Zinc transport protein ZntB / Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle ...Zinc transport protein ZntB / Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / CorA, cytoplasmic domain / CorA, transmembrane region / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Zinc transport protein ZntB
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsWan, Q. / Dealwis, C.
CitationJournal: TO BE PUBLISHED
Title: The Soluble Domain Structure of the ZntB Zn2+ Efflux System
Authors: Wan, Q. / Gorzelle, B. / Fairman, J.W. / Fuente, M. / Homammed, F. / Dealwis, C. / Maguire, M.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 17, 2016Group: Structure summary
Revision 1.3Feb 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_ref_seq_dif / 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_asym_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_ref_seq_dif.details / _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: Zinc transport protein zntB
B: Zinc transport protein zntB
C: Zinc transport protein zntB
D: Zinc transport protein zntB
E: Zinc transport protein zntB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,78520
Polymers148,8045
Non-polymers98115
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.570, 101.944, 90.288
Angle α, β, γ (deg.)90.000, 110.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-266-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISILEILEchain A and (resseq 2:95 or resseq 106:177 or resseq 182:259 )AA2 - 951 - 94
12LEULEUASNASNchain A and (resseq 2:95 or resseq 106:177 or resseq 182:259 )AA106 - 177105 - 176
13GLNGLNGLNGLNchain A and (resseq 2:95 or resseq 106:177 or resseq 182:259 )AA182 - 259181 - 258
21HISHISILEILEchain B and (resseq 2:95 or resseq 106:177 or resseq 182:259 )BB2 - 951 - 94
22LEULEUASNASNchain B and (resseq 2:95 or resseq 106:177 or resseq 182:259 )BB106 - 177105 - 176
23GLNGLNGLNGLNchain B and (resseq 2:95 or resseq 106:177 or resseq 182:259 )BB182 - 259181 - 258
31HISHISILEILEchain C and (resseq 2:95 or resseq 106:177 or resseq 182:259 )CC2 - 951 - 94
32LEULEUASNASNchain C and (resseq 2:95 or resseq 106:177 or resseq 182:259 )CC106 - 177105 - 176
33GLNGLNGLNGLNchain C and (resseq 2:95 or resseq 106:177 or resseq 182:259 )CC182 - 259181 - 258
41HISHISILEILEchain D and (resseq 2:95 or resseq 106:177 or resseq 182:259 )DD2 - 951 - 94
42LEULEUASNASNchain D and (resseq 2:95 or resseq 106:177 or resseq 182:259 )DD106 - 177105 - 176
43GLNGLNGLNGLNchain D and (resseq 2:95 or resseq 106:177 or resseq 182:259 )DD182 - 259181 - 258
51HISHISILEILEchain E and (resseq 2:95 or resseq 106:177 or resseq 182:259 )EE2 - 951 - 94
52LEULEUASNASNchain E and (resseq 2:95 or resseq 106:177 or resseq 182:259 )EE106 - 177105 - 176
53GLNGLNGLNGLNchain E and (resseq 2:95 or resseq 106:177 or resseq 182:259 )EE182 - 259181 - 258

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Components

#1: Protein
Zinc transport protein zntB


Mass: 29760.775 Da / Num. of mol.: 5 / Fragment: soluble domain (unp residues 1-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: subsp. enterica serovar Typhimurium / Gene: zntB, STM1656 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EYX5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30-35% PEG 3350, 0.1 M Tris pH8.5, 0.2 M (NH4)2SO4, 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: 1.282 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.13→49 Å / Num. obs: 25929 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 70.46 Å2 / Rsym value: 0.092
Reflection shellResolution: 3.13→3.17 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→48.567 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.88 / σ(F): 0.08 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 3619 7.67 %RANDOM
Rwork0.2127 ---
obs0.2168 24662 92.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.272 e/Å3
Displacement parametersBiso max: 277.26 Å2 / Biso mean: 102.9096 Å2 / Biso min: 19.37 Å2
Baniso -1Baniso -2Baniso -3
1--26.0413 Å2-0 Å2-19.4169 Å2
2---3.8818 Å20 Å2
3---2.0896 Å2
Refinement stepCycle: LAST / Resolution: 3.13→48.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9551 0 15 0 9566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019721
X-RAY DIFFRACTIONf_angle_d1.28213186
X-RAY DIFFRACTIONf_chiral_restr0.0821488
X-RAY DIFFRACTIONf_plane_restr0.0041737
X-RAY DIFFRACTIONf_dihedral_angle_d18.7063580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1885X-RAY DIFFRACTIONPOSITIONAL0.05
12B1885X-RAY DIFFRACTIONPOSITIONAL0.05
13C1885X-RAY DIFFRACTIONPOSITIONAL0.057
14D1885X-RAY DIFFRACTIONPOSITIONAL0.056
15E1885X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1308-3.17190.39311040.35451180128466
3.1719-3.21540.46661240.3481543166785
3.2154-3.26130.41981340.31331622175689
3.2613-3.310.37621350.27151682181793
3.31-3.36170.27881470.25921687183492
3.3617-3.41680.38091350.25981653178891
3.4168-3.47570.3471280.26041595172387
3.4757-3.53890.31121370.24541605174289
3.5389-3.60690.33271360.22941707184394
3.6069-3.68050.29391490.23661772192198
3.6805-3.76050.26861530.21331820197398
3.7605-3.8480.27791330.20311651178494
3.848-3.94420.25061340.2021629176390
3.9442-4.05070.20931350.2031593172886
4.0507-4.16990.24351280.18861595172389
4.1699-4.30440.23321470.18011671181893
4.3044-4.45810.21231420.15791740188297
4.4581-4.63650.20081460.13441732187895
4.6365-4.84730.17661410.13481745188695
4.8473-5.10260.24031430.15491757190096
5.1026-5.42190.25081510.18461725187696
5.4219-5.83990.22781470.20751754190198
5.8399-6.42640.26891520.20561805195798
6.4264-7.35360.27591420.17521784192698
7.3536-9.25430.18611500.17391793194398
9.2543-48.57240.22381460.22891698184494
Refinement TLS params.Method: refined / Origin x: 37.2403 Å / Origin y: 47.5873 Å / Origin z: -28.3714 Å
111213212223313233
T0.3251 Å2-0.0003 Å20.2146 Å2-0.062 Å20.0241 Å2--0.039 Å2
L1.7352 °20.1522 °20.6263 °2--0.1878 °2-0.0615 °2--0.1657 °2
S-0.0273 Å °-0.1131 Å °-0.1038 Å °0.0295 Å °-0.0169 Å °-0.0468 Å °-0.0848 Å °0.0547 Å °0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 260
2X-RAY DIFFRACTION1allB2 - 262
3X-RAY DIFFRACTION1allC2 - 264
4X-RAY DIFFRACTION1allD2 - 264
5X-RAY DIFFRACTION1allE2 - 263
6X-RAY DIFFRACTION1allA - E1 - 267

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