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

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Basic information

Entry
Database: PDB / ID: 3nvo
TitleThe Soluble Domain Structure of the ZntB Zn2+ Efflux System
ComponentsZinc transport protein zntB
KeywordsTRANSPORT PROTEIN / alpha-beta-alpha sandwich / zinc efflux system / 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: 2.3 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. / Fuente, M. / Mohammed, F. / Dealwis, C. / Maguire, M.
History
DepositionJul 8, 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 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _struct_conn.ptnr2_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54314
Polymers59,6362
Non-polymers90812
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Zinc transport protein zntB
hetero molecules

B: Zinc transport protein zntB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,54314
Polymers59,6362
Non-polymers90812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2570 Å2
ΔGint-325 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.039, 93.845, 68.231
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Zinc transport protein zntB


Mass: 29817.826 Da / Num. of mol.: 2 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4249.11
2
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30-35% PEG 3350, 0.1 M Tris, pH 8.5, 500 mM NaCl and 0.2 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 25345 / Num. obs: 24331 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 36.33 Å2 / Rsym value: 0.085
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 2.1 % / Rsym value: 0.49 / % possible all: 74.4

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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: 2.3→38.658 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.79 / σ(F): 0.1 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1236 5.64 %RANDOM
Rwork0.2013 ---
obs0.204 21908 86.71 %-
all-24331 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.118 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 158.64 Å2 / Biso mean: 48.6333 Å2 / Biso min: 12.94 Å2
Baniso -1Baniso -2Baniso -3
1-9.1157 Å20 Å20.3578 Å2
2--1.1527 Å2-0 Å2
3----10.2684 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 28 104 3935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053884
X-RAY DIFFRACTIONf_angle_d0.8345271
X-RAY DIFFRACTIONf_chiral_restr0.055596
X-RAY DIFFRACTIONf_plane_restr0.003691
X-RAY DIFFRACTIONf_dihedral_angle_d16.5031412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.39210.29311230.2272008213176
2.3921-2.50090.32261160.23761899201571
2.5009-2.63280.37211140.23521993210776
2.6328-2.79770.30231170.2572081219879
2.7977-3.01360.33241370.24932215235284
3.0136-3.31670.28971600.22022529268996
3.3167-3.79630.23551510.176626662817100
3.7963-4.78150.19621560.15762605276198
4.7815-38.66320.2271620.18782676283899
Refinement TLS params.Method: refined / Origin x: 26.4767 Å / Origin y: 66.9951 Å / Origin z: 3.5597 Å
111213212223313233
T0.1501 Å2-0.0166 Å2-0.0208 Å2-0.1502 Å20.0011 Å2--0.1344 Å2
L0.6299 °2-0.4255 °20.0886 °2-0.8069 °2-0.2385 °2--0.5022 °2
S0.0106 Å °0.1304 Å °-0.0296 Å °0.0054 Å °-0.0465 Å °0.0375 Å °-0.1081 Å °0.0184 Å °0.035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 264
2X-RAY DIFFRACTION1allB1 - 260
3X-RAY DIFFRACTION1allA4 - 336
4X-RAY DIFFRACTION1all1 - 4
5X-RAY DIFFRACTION1allB - A1 - 271

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