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

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Basic information

Entry
Database: PDB / ID: 4rdt
TitleStructure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (flexible conformation bound to a zinc ion)
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 / metal ion binding
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Probable TonB-dependent receptor NMB0964
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsCalmettes, C. / El Bakkouri, M. / 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
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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: ZnuD
B: ZnuD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,88111
Polymers168,6692
Non-polymers1,2129
Water19811
1
A: ZnuD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3858
Polymers84,3351
Non-polymers1,0517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ZnuD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4963
Polymers84,3351
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.340, 156.227, 158.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ZnuD


Mass: 84334.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (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 , 5 types, 20 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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 Hepes pH 7.2, 1M Magnesium Sulfate, vapor diffusion, hanging drop, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC Q315 detector / Detector: CCD / Date: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 50916 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 77.97 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.19-3.2380.661199.8
3.23-3.288.10.541199.9
3.28-3.3380.561199.8
3.33-3.388.10.461100
3.38-3.438.10.4461100
3.43-3.498.20.3431100
3.49-3.568.10.336199.9
3.56-3.638.20.251100
3.63-3.78.20.2991100
3.7-3.788.30.2621100
3.78-3.878.30.2061100
3.87-3.968.30.193199.9
3.96-4.078.40.1741100
4.07-4.198.40.1641100
4.19-4.338.40.1321100
4.33-4.488.30.1141100
4.48-4.668.20.1021100
4.66-4.878.30.1061100
4.87-5.138.20.1151100
5.13-5.458.20.1191100
5.45-5.878.10.1111100
5.87-6.4680.0971100
6.46-7.397.70.0811100
7.39-9.37.70.0621100
9.3-506.80.048198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.928 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 38.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3047 1646 3.94 %
Rwork0.2704 --
obs0.2718 41783 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.3669 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 72 11 10151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810367
X-RAY DIFFRACTIONf_angle_d1.55213981
X-RAY DIFFRACTIONf_dihedral_angle_d17.0053840
X-RAY DIFFRACTIONf_chiral_restr0.0961441
X-RAY DIFFRACTIONf_plane_restr0.0061845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.29420.36841420.31193300X-RAY DIFFRACTION99
3.2942-3.40050.33521360.30553281X-RAY DIFFRACTION99
3.4005-3.5220.34831410.28243301X-RAY DIFFRACTION99
3.522-3.66290.31131340.29383301X-RAY DIFFRACTION99
3.6629-3.82960.30961360.26723322X-RAY DIFFRACTION100
3.8296-4.03140.28881340.273330X-RAY DIFFRACTION99
4.0314-4.28390.27391350.26073354X-RAY DIFFRACTION100
4.2839-4.61440.3031370.23573350X-RAY DIFFRACTION100
4.6144-5.07840.2591370.23383365X-RAY DIFFRACTION100
5.0784-5.81230.31171360.26613392X-RAY DIFFRACTION100
5.8123-7.31920.32461380.28323413X-RAY DIFFRACTION100
7.3192-49.93440.30811400.28673428X-RAY DIFFRACTION95
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)
12.1895-0.00730.54291.32541.01481.72240.1336-0.3775-1.1260.24830.0222-0.36740.49440.0329-0.040.30530.03520.10830.52650.22431.531514.72844.99773.289
20.61410.0118-0.1117.407-1.66251.4686-0.3572-0.0894-0.6798-0.06230.26211.15140.3299-0.66-0.28050.23230.00810.01420.50890.11360.7814-0.58848.69173.927
30.7886-0.6715-1.82019.26046.54567.0863-0.33311.7408-0.266-1.9070.28510.5145-0.4438-1.43850.16521.4185-0.27370.14452.0112-0.31140.922811.81664.3538.465
42.62-0.58710.01822.2152-0.48120.7636-0.0420.198-0.8293-0.1811-0.4673-1.04490.11260.29960.14150.31650.0139-0.03690.4427-0.00220.662718.83248.569.238
50.23790.06860.09370.27690.34280.4351-0.28420.09040.1296-1.1260.03260.2368-0.024-0.2349-0.3571.3214-0.0749-0.13332.223-0.73420.6304-14.71944.9825.72
60.7822-0.23440.65026.71081.81431.1086-0.0150.64610.0951-2.205-0.0725-0.9171-0.46480.1105-0.08131.54060.21180.2072.3122-0.63591.23920.6748.5194.759
71.9106-0.6347-1.65453.9591-1.71153.6733-0.13360.46190.48490.4147-0.1667-0.8104-0.4721-1.03640.27231.23640.3525-0.60511.2008-0.42411.2178-11.81764.30740.574
82.99940.3023-0.16452.8814-0.72970.18170.00060.81-0.3606-0.9025-0.12970.0373-0.08410.10760.10121.38020.0466-0.08641.9825-0.88361.4176-18.84648.5169.784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:145 )A20 - 145
2X-RAY DIFFRACTION2( CHAIN A AND RESID 146:241 )A146 - 241
3X-RAY DIFFRACTION3( CHAIN A AND RESID 248:287 )A248 - 287
4X-RAY DIFFRACTION4( CHAIN A AND RESID 300:734 )A300 - 734
5X-RAY DIFFRACTION5( CHAIN B AND RESID 20:145 )B20 - 145
6X-RAY DIFFRACTION6( CHAIN B AND RESID 146:240 )B146 - 240
7X-RAY DIFFRACTION7( CHAIN B AND RESID 248:287 )B248 - 287
8X-RAY DIFFRACTION8( CHAIN B AND ( RESID 299:734 OR RESID 801:802 OR RESID 901:902 ) )B299 - 734
9X-RAY DIFFRACTION8( CHAIN B AND ( RESID 299:734 OR RESID 801:802 OR RESID 901:902 ) )B801 - 802
10X-RAY DIFFRACTION8( CHAIN B AND ( RESID 299:734 OR RESID 801:802 OR RESID 901:902 ) )B901 - 902

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