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- PDB-4k0e: X-ray crystal structure of a heavy metal efflux pump, crystal form II -

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Basic information

Entry
Database: PDB / ID: 4k0e
TitleX-ray crystal structure of a heavy metal efflux pump, crystal form II
ComponentsHeavy metal cation tricomponent efflux pump ZneA(CzcA-like)
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Center for Structures of Membrane Proteins / CSMP / Resistance-nodulation-cell division (RND) superfamily / Heavy metal efflux pump / ZneB / ZneC / Inner membrane
Function / homologyCation efflux system CzcA/CusA/SilA/NccA/HelA/CnrA / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / monoatomic cation transmembrane transporter activity / membrane / Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
Function and homology information
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.713 Å
AuthorsPak, J.E. / Ngonlong Ekende, E. / Vandenbussche, G. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter.
Authors: Pak, J.E. / Ekende, E.N. / Kifle, E.G. / O'Connell, J.D. / De Angelis, F. / Tessema, M.B. / Derfoufi, K.M. / Robles-Colmenares, Y. / Robbins, R.A. / Goormaghtigh, E. / Vandenbussche, G. / Stroud, R.M.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references / Structure summary
Revision 1.2Nov 6, 2013Group: Structure summary
Revision 1.3Dec 4, 2013Group: Database references
Revision 1.4Dec 11, 2013Group: Structure summary
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
B: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
C: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,8557
Polymers343,5933
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-169 kcal/mol
Surface area115530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.342, 127.068, 163.331
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)


Mass: 114531.086 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: zneA / Production host: Escherichia coli (E. coli) / References: UniProt: Q1LCD8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG 400, 100 mM Na HEPES, 100 mM MgCl2, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3.7→20 Å / Num. all: 44709 / Num. obs: 43547 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rsym value: 0.123 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.7-3.832.41.50.678198.6
7.83-202.529.70.026195
6.27-7.832.411.90.078196
5.5-6.272.56.10.156196.6
5.01-5.52.56.50.146197.4
4.65-5.012.56.20.154197.8
4.38-4.652.45.40.179198.1
4.16-4.382.54.10.258198.2
3.98-4.162.52.70.376198.5
3.83-3.982.41.90.516198.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ZneA, crystal form I

Resolution: 3.713→19.942 Å / SU ML: 0.53 / σ(F): 1.42 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 2041 4.87 %Random
Rwork0.2291 ---
obs0.2317 41878 --
all-44707 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.713→19.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22057 0 4 0 22061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322433
X-RAY DIFFRACTIONf_angle_d0.81730504
X-RAY DIFFRACTIONf_dihedral_angle_d11.7648214
X-RAY DIFFRACTIONf_chiral_restr0.0553694
X-RAY DIFFRACTIONf_plane_restr0.0043894
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.713-3.79880.39651150.30862021202169.6
3.7988-3.89320.31541130.27812474247484.2
3.8932-3.99760.29811450.27512491249186
3.9976-4.11420.33321430.25422581258189
4.1142-4.24580.27761320.24742673267391.4
4.2458-4.3960.2791460.21762696269692.2
4.396-4.570.28131340.2172749274993.3
4.57-4.77530.29181390.2022709270992.7
4.7753-5.02320.25571530.20682725272593.5
5.0232-5.33230.27961220.21452760276093.8
5.3323-5.73490.31421330.24312793279393.9
5.7349-6.29550.31291640.26292743274393.9
6.2955-7.16910.36321080.25482804280494.4
7.1691-8.89680.22781500.19582775277593.7
8.8968-19.9420.25031440.21312843284394.4
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)
14.6118-0.035-0.65831.8637-0.30462.1511-0.1597-1.1871-0.27370.3634-0.10540.67070.0086-0.53210.25110.7021-0.06980.10771.3126-0.14981.1176-2.7827-37.392639.0214
23.941-1.3993-1.75781.23490.80181.15650.2566-0.78590.21640.34570.00780.4503-0.4023-0.503-0.19871.32110.02390.28211.4586-0.12561.025115.4824.866658.3683
33.11210.6514-1.7772.3773-1.10151.80720.0837-0.6333-0.00550.9417-0.04940.53540.078-0.01060.14561.4238-0.15390.1781.66610.29831.065629.5908-41.633876.5023
42.0478-0.1097-0.36982.20480.69961.6583-0.03490.1049-0.1195-0.14750.03320.12470.10480.0130.0390.69260.0243-0.13390.5705-0.01920.629530.0878-37.30811.7385
51.69880.005-0.44792.5031-0.53213.14690.3271-0.34620.1915-0.0912-0.1306-0.163-0.6502-0.1589-0.15820.8402-0.1040.07440.679-0.08260.660948.23673.515932.1431
63.67190.08860.96513.24860.08842.30090.1146-0.3385-0.04230.0685-0.374-0.60860.55210.66170.06830.92250.0547-0.02391.13130.29990.823762.2824-40.882949.5503
70.0007-0.05110.14212.10120.85670.91080.01310.0962-0.1811-1.1720.1379-0.822-0.21110.315-0.27061.6805-0.16310.31261.0114-0.06041.236358.126-27.6557-2.3019
80.56360.0622-1.16641.0181-0.99172.92130.008-0.3339-0.0614-0.4808-0.2759-0.46180.0150.91770.24830.9554-0.0690.1410.89160.09511.186773.588-8.835315.6465
91.3457-0.00881.66340.07160.12721.7878-0.33010.0743-0.17170.15010.284-0.63610.09480.54110.04271.2330.4323-0.01821.4099-0.00941.172476.4261-38.700120.7637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 4:36 or resid 323:550 or resid 851:1006)A4 - 36
2X-RAY DIFFRACTION1chain A and (resid 4:36 or resid 323:550 or resid 851:1006)A323 - 550
3X-RAY DIFFRACTION1chain A and (resid 4:36 or resid 323:550 or resid 851:1006)A851 - 1006
4X-RAY DIFFRACTION2chain B and (resid 4:36 or resid 323:550 or resid 851:1006)B4 - 36
5X-RAY DIFFRACTION2chain B and (resid 4:36 or resid 323:550 or resid 851:1006)B323 - 550
6X-RAY DIFFRACTION2chain B and (resid 4:36 or resid 323:550 or resid 851:1006)B851 - 1006
7X-RAY DIFFRACTION3chain C and (resid 4:36 or resid 323:550 or resid 851:1006)C4 - 36
8X-RAY DIFFRACTION3chain C and (resid 4:36 or resid 323:550 or resid 851:1006)C323 - 550
9X-RAY DIFFRACTION3chain C and (resid 4:36 or resid 323:550 or resid 851:1006)C851 - 1006
10X-RAY DIFFRACTION4chain A and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)A37 - 182
11X-RAY DIFFRACTION4chain A and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)A267 - 322
12X-RAY DIFFRACTION4chain A and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)A551 - 697
13X-RAY DIFFRACTION4chain A and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)A797 - 850
14X-RAY DIFFRACTION5chain B and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)B37 - 182
15X-RAY DIFFRACTION5chain B and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)B267 - 322
16X-RAY DIFFRACTION5chain B and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)B551 - 697
17X-RAY DIFFRACTION5chain B and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)B797 - 850
18X-RAY DIFFRACTION6chain C and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)C37 - 182
19X-RAY DIFFRACTION6chain C and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)C267 - 322
20X-RAY DIFFRACTION6chain C and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)C551 - 697
21X-RAY DIFFRACTION6chain C and (resid 37:182 or resid 267:322 or resid 551:697 or resid 797:850)C797 - 850
22X-RAY DIFFRACTION7chain A and (resid 183:266 or resid 698:796)A183 - 266
23X-RAY DIFFRACTION7chain A and (resid 183:266 or resid 698:796)A698 - 796
24X-RAY DIFFRACTION8chain B and (resid 183:266 or resid 698:796)B183 - 266
25X-RAY DIFFRACTION8chain B and (resid 183:266 or resid 698:796)B698 - 796
26X-RAY DIFFRACTION9chain C and (resid 183:266 or resid 698:796)C183 - 266
27X-RAY DIFFRACTION9chain C and (resid 183:266 or resid 698:796)C698 - 796

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