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- PDB-4rdr: Structure of the bacterial Zn-transporter ZnuD from Neisseria men... -

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Basic information

Entry
Database: PDB / ID: 4rdr
TitleStructure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked conformation bound to zinc and cadmium ions)
ComponentsZnuD
KeywordsMEMBRANE PROTEIN / Outer membrane protein / Zinc transporter / Zinc acquisition / TonB dependent receptor / vaccine candidate
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / cell outer membrane
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB-dependent receptor (TBDR) proteins profile. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB-dependent receptor (TBDR) proteins profile. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
: / Probable TonB-dependent receptor NMB0964
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.472 Å
AuthorsCalmettes, C. / Moraes, T.F.
CitationJournal: Nat Commun / Year: 2015
Title: The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD.
Authors: Calmettes, C. / Ing, C. / Buckwalter, C.M. / El Bakkouri, M. / Chieh-Lin Lai, C. / Pogoutse, A. / Gray-Owen, S.D. / Pomes, R. / Moraes, T.F.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZnuD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,22839
Polymers84,7101
Non-polymers4,51838
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.073, 155.819, 159.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ZnuD


Mass: 84709.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Strain: MC58 / Gene: NMB0964 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JZN9

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Non-polymers , 7 types, 133 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M sodium cacodylate pH 6.6, 0.4M Magnesium Sulfate, 2% (w/v) Ethylene glycol, 0.7mM Cadmium chloride, vapor diffusion, hanging drop, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 45376 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 54.72 Å2 / Rmerge(I) obs: 0.113 / Χ2: 2.681 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.47-2.536.70.96329661.1021100
2.53-2.597.50.81430051.1031100
2.59-2.668.70.72630131.1191100
2.66-2.74100.61629661.1681100
2.74-2.8311.60.49329911.2121100
2.83-2.9312.60.38730171.2861100
2.93-3.0513.80.32830011.3931100
3.05-3.18150.26930031.6221100
3.18-3.3514.90.20129972.0391100
3.35-3.5614.70.16230262.5041100
3.56-3.8414.60.11830292.9241100
3.84-4.2214.30.08930403.4041100
4.22-4.8313.40.07630524.6561100
4.83-6.0913.30.07730785.1931100
6.09-5012.30.06531926.809199.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.472→39.981 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 3844 4.42 %
Rwork0.2181 --
obs0.2193 -99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.32 Å2 / Biso mean: 91.4041 Å2 / Biso min: 46.87 Å2
Refinement stepCycle: LAST / Resolution: 2.472→39.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 257 95 5974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076003
X-RAY DIFFRACTIONf_angle_d1.1728079
X-RAY DIFFRACTIONf_chiral_restr0.077799
X-RAY DIFFRACTIONf_plane_restr0.0051043
X-RAY DIFFRACTIONf_dihedral_angle_d16.3172242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4718-2.50310.36671470.36793015316299
2.5031-2.5360.34811450.330530983243100
2.536-2.57070.33331280.318830693197100
2.5707-2.60740.36271460.309531103256100
2.6074-2.64640.29911450.304430753220100
2.6464-2.68770.3341450.289630743219100
2.6877-2.73170.31541370.282531263263100
2.7317-2.77880.29131400.264430493189100
2.7788-2.82940.27521500.261830523202100
2.8294-2.88380.2751450.26330713216100
2.8838-2.94260.27631390.248831083247100
2.9426-3.00660.27391470.254330543201100
3.0066-3.07650.24541500.250131063256100
3.0765-3.15340.27711310.229831023233100
3.1534-3.23860.25911430.221130493192100
3.2386-3.33390.23571390.222530983237100
3.3339-3.44140.26581470.220830443191100
3.4414-3.56430.25051420.215231063248100
3.5643-3.7070.22541490.203831183267100
3.707-3.87550.24281390.201630353174100
3.8755-4.07970.24551400.20331283268100
4.0797-4.3350.21791410.190830533194100
4.335-4.66920.18841420.167630883230100
4.6692-5.13830.19821400.175430993239100
5.1383-5.87980.21091350.198331093244100
5.8798-7.40020.23151420.218530633205100
7.4002-39.98630.2891500.215830853235100
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)
10.1399-0.0496-0.15690.5387-0.26980.4086-0.0558-0.65870.56330.1114-0.0990.0965-0.06040.0842-0.050.5767-0.0174-0.05090.7747-0.39950.7867-34.11237.23131.244
21.67670.14440.58380.56360.09380.92910.0188-0.52540.1961-0.046-0.11930.18230.1017-0.2054-0.0240.5869-0.0030.00260.715-0.27120.6274-44.01227.12629.913
32.2363-0.5957-0.24230.2735-0.27770.96130.0074-0.6105-0.25770.09220.1054-0.07850.27360.1684-0.00870.67510.0497-0.04720.8172-0.15390.5615-29.47218.137.338
41.44420.25260.50491.0034-0.16610.7788-0.13040.05640.3105-0.19040.1106-0.0973-0.05210.378-0.05230.5826-0.0418-0.00210.5221-0.20330.6003-29.49734.11419.128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:90 )A18 - 90
2X-RAY DIFFRACTION2( CHAIN A AND RESID 91:363 )A91 - 363
3X-RAY DIFFRACTION3( CHAIN A AND RESID 364:486 )A364 - 486
4X-RAY DIFFRACTION4( CHAIN A AND RESID 487:734 )A487 - 734

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