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- PDB-4k0j: X-ray crystal structure of a heavy metal efflux pump, crystal form I -

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Basic information

Entry
Database: PDB / ID: 4k0j
TitleX-ray crystal structure of a heavy metal efflux pump, crystal form I
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 Å
AuthorsPak, J.E. / Stroud, R.M. / Ngonlong Ekende, E. / Vandenbussche, G. / 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 4, 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 1.4Sep 20, 2023Group: 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_initial_refinement_model / 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

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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)
D: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
E: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
F: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)687,44810
Polymers687,1876
Non-polymers2624
Water0
1
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)343,7245
Polymers343,5933
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-118 kcal/mol
Surface area115210 Å2
MethodPISA
2
D: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
E: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
F: Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,7245
Polymers343,5933
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-120 kcal/mol
Surface area115200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.627, 129.056, 392.374
Angle α, β, γ (deg.)90.00, 94.62, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain D
112chain B
212chain E
113chain C
213chain F

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 114531.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: zneA, Rmet_5329 / 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: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 26% PEG 400, 100 mM ADA, 100 mM LiSO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 219457 / Num. obs: 214382 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.109 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3-3.112.71.80.661199.6
5.11-6.42.814.40.075197.2
4.47-5.112.714.10.073198
4.06-4.472.712.50.086198.4
3.78-4.062.78.70.13198.8
3.55-3.782.76.60.178199.1
3.38-3.552.74.80.243199.3
3.23-3.382.73.20.358199.4
3.11-3.232.72.30.512199.6
6.4-202.921.80.047195.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NE5, Chain A

3ne5


Resolution: 3→19.978 Å / SU ML: 0.53 / σ(F): 1.42 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3055 1895 0.88 %Random
Rwork0.2786 ---
obs0.2789 213992 97.33 %-
all-219457 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44014 0 4 0 44018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444754
X-RAY DIFFRACTIONf_angle_d0.86160860
X-RAY DIFFRACTIONf_dihedral_angle_d13.43216368
X-RAY DIFFRACTIONf_chiral_restr0.0577384
X-RAY DIFFRACTIONf_plane_restr0.0047768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7336X-RAY DIFFRACTIONPOSITIONAL
12D7336X-RAY DIFFRACTIONPOSITIONAL0.012
21B7314X-RAY DIFFRACTIONPOSITIONAL
22E7314X-RAY DIFFRACTIONPOSITIONAL0.012
31C7357X-RAY DIFFRACTIONPOSITIONAL
32F7357X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3-3.07480.34181200.3341145531455393
3.0748-3.15760.3681530.3311148391483995
3.1576-3.25010.36131170.3253151931519397
3.2501-3.35460.37191440.3144152791527998
3.3546-3.47390.3151190.3034155141551499
3.4739-3.61220.34071570.2953154411544199
3.6122-3.77550.33631130.288155111551199
3.7755-3.97310.33281570.2859154291542999
3.9731-4.21980.28541470.2666154821548299
4.2198-4.54210.2964900.254154531545398
4.5421-4.99270.29311980.2546153991539998
4.9927-5.70050.31051650.2678152981529897
5.7005-7.12740.3266330.2958154431544397
7.1274-19.97860.24751820.2514151581515895
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)
11.5242-0.8836-0.44960.95710.71070.8545-0.1274-0.6667-0.0240.36440.2667-0.1803-0.49970.0986-0.04380.8156-0.0085-0.09590.86560.01860.275763.504137.065767.4815
21.1663-0.4882-0.9940.9442-0.36271.79260.23330.7308-0.0193-0.6368-0.17080.0298-0.52940.5062-0.04631.0506-0.1591-0.11780.96250.05660.230318.905362.6961128.0477
31.36590.76310.60080.66520.12191.24990.3129-0.60040.00320.4104-0.2531-0.06820.30110.1151-0.04240.98640.13480.09150.82330.06080.421635.1839-4.542268.164
40.0336-0.27350.67351.832-0.5921.603-0.0555-0.26280.36440.91860.00270.39930.1707-1.04480.09171.0146-0.215-0.05131.1377-0.20110.034912.725941.751768.4655
50.2767-0.47390.36121.5192-0.01260.52770.07330.361-0.0441-0.5438-0.0069-0.08280.0725-0.191-0.07240.6536-0.08570.04420.9643-0.04180.4298-2.853517.4701127.4235
60.86290.64480.27291.1510.77770.8775-0.06260.68170.0688-0.27320.0292-0.09730.75150.1390.01210.96140.06050.11740.72650.04380.295148.547920.9999127.0836
70.45731.211-0.44531.8443-1.12781.43190.18770.1520.09610.35620.00070.4225-0.38470.137-0.05620.3008-0.07270.00340.25730.08190.452562.815337.501425.846
80.2003-0.6406-0.55521.48171.29732.0991-0.2513-0.49010.23210.24030.3811-0.1110.26550.2832-0.04070.26140.04510.08170.2756-0.0040.345935.1192-4.035926.2254
92.35550.3110.72880.68540.0491.37950.1355-0.2301-0.25780.3734-0.0207-0.15510.217-0.3254-0.04350.21370.0011-0.0830.4094-0.05720.346513.217741.250826.2085
101.02851.02861.38572.11681.19992.2763-0.21590.3921-0.2002-0.07860.3224-0.4033-0.4640.34260.0170.4573-0.0868-0.07880.1735-0.02760.430919.628662.3276169.6827
112.1296-0.2525-1.4955-0.17390.60911.50820.21780.36120.3948-0.264-0.0568-0.2404-0.1234-0.4267-0.0420.21550.00960.01440.3044-0.0470.41-2.40117.626169.3632
120.9942-0.75850.29091.7356-1.28411.96950.05750.0003-0.0108-0.35980.1630.05460.38780.0506-0.0340.3646-0.00730.02630.18560.07410.329447.782621.1917169.3384
130.5970.2917-0.58292.5114-1.2932-0.5556-0.05950.19420.0004-0.58010.0695-0.04270.21870.0653-0.03420.4976-0.08210.00990.3441-0.06740.404954.580427.6993-4.6213
140.091-0.5675-0.28651.37870.8105-0.93140.0750.054-0.1819-0.3808-0.0540.1813-0.08560.0262-0.05920.3290.02740.00690.3226-0.02820.506131.38158.4291-4.2099
151.08470.23550.8831-0.47150.1885-0.72360.09190.4391-0.15220.25840.0274-0.1432-0.07640.19410.1020.2406-0.009-0.01420.68-0.02290.514725.761538.3599-4.268
160.3161-0.03160.92970.61171.0478-0.70140.0817-0.21140.02470.1713-0.0965-0.03350.1977-0.4440.00670.4614-0.1112-0.00570.3618-0.06450.508215.302350.2827200.1515
171.5734-0.111-1.04260.267-0.1619-0.79050.0583-0.4548-0.03140.0847-0.08460.15430.1923-0.02490.02270.35010.07810.07970.48350.00390.431710.255320.5606199.8058
180.1251-0.2083-0.03421.9361-1.1347-1.8542-0.2160.00030.13540.04340.77-0.6992-0.05590.68340.16970.38670.158-0.09120.26970.10840.293338.9530.6259199.7942
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 D and (resid 4:36 or resid 323:550 or resid 851:1006)D4 - 36
5X-RAY DIFFRACTION2chain D and (resid 4:36 or resid 323:550 or resid 851:1006)D323 - 550
6X-RAY DIFFRACTION2chain D and (resid 4:36 or resid 323:550 or resid 851:1006)D851 - 1006
7X-RAY DIFFRACTION3chain B and (resid 4:36 or resid 323:550 or resid 851:1006)B4 - 36
8X-RAY DIFFRACTION3chain B and (resid 4:36 or resid 323:550 or resid 851:1006)B323 - 550
9X-RAY DIFFRACTION3chain B and (resid 4:36 or resid 323:550 or resid 851:1006)B851 - 1006
10X-RAY DIFFRACTION4chain C and (resid 4:36 or resid 323:550 or resid 851:1006)C4 - 36
11X-RAY DIFFRACTION4chain C and (resid 4:36 or resid 323:550 or resid 851:1006)C323 - 550
12X-RAY DIFFRACTION4chain C and (resid 4:36 or resid 323:550 or resid 851:1006)C851 - 1006
13X-RAY DIFFRACTION5chain E and (resid 4:36 or resid 323:550 or resid 851:1006)E4 - 36
14X-RAY DIFFRACTION5chain E and (resid 4:36 or resid 323:550 or resid 851:1006)E323 - 550
15X-RAY DIFFRACTION5chain E and (resid 4:36 or resid 323:550 or resid 851:1006)E851 - 1006
16X-RAY DIFFRACTION6chain F and (resid 4:36 or resid 323:550 or resid 851:1006)F4 - 36
17X-RAY DIFFRACTION6chain F and (resid 4:36 or resid 323:550 or resid 851:1006)F323 - 550
18X-RAY DIFFRACTION6chain F and (resid 4:36 or resid 323:550 or resid 851:1006)F851 - 1006
19X-RAY DIFFRACTION7chain A and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)A37 - 182
20X-RAY DIFFRACTION7chain A and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)A277 - 322
21X-RAY DIFFRACTION7chain A and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)A551 - 697
22X-RAY DIFFRACTION7chain A and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)A797 - 850
23X-RAY DIFFRACTION8chain B and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)B37 - 182
24X-RAY DIFFRACTION8chain B and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)B277 - 322
25X-RAY DIFFRACTION8chain B and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)B551 - 697
26X-RAY DIFFRACTION8chain B and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)B797 - 850
27X-RAY DIFFRACTION9chain C and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)C37 - 182
28X-RAY DIFFRACTION9chain C and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)C277 - 322
29X-RAY DIFFRACTION9chain C and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)C551 - 697
30X-RAY DIFFRACTION9chain C and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)C797 - 850
31X-RAY DIFFRACTION10chain D and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)D37 - 182
32X-RAY DIFFRACTION10chain D and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)D277 - 322
33X-RAY DIFFRACTION10chain D and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)D551 - 697
34X-RAY DIFFRACTION10chain D and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)D797 - 850
35X-RAY DIFFRACTION11chain E and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)E37 - 182
36X-RAY DIFFRACTION11chain E and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)E277 - 322
37X-RAY DIFFRACTION11chain E and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)E551 - 697
38X-RAY DIFFRACTION11chain E and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)E797 - 850
39X-RAY DIFFRACTION12chain F and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)F37 - 182
40X-RAY DIFFRACTION12chain F and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)F277 - 322
41X-RAY DIFFRACTION12chain F and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)F551 - 697
42X-RAY DIFFRACTION12chain F and (resid 37:182 or resid 277:322 or resid 551:697 or resid 797:850)F797 - 850
43X-RAY DIFFRACTION13chain A and (resid 183:266 or resid 698:796)A183 - 266
44X-RAY DIFFRACTION13chain A and (resid 183:266 or resid 698:796)A698 - 796
45X-RAY DIFFRACTION14chain B and (resid 183:266 or resid 698:796)B183 - 266
46X-RAY DIFFRACTION14chain B and (resid 183:266 or resid 698:796)B698 - 796
47X-RAY DIFFRACTION15chain C and (resid 183:266 or resid 698:796)C183 - 266
48X-RAY DIFFRACTION15chain C and (resid 183:266 or resid 698:796)C698 - 796
49X-RAY DIFFRACTION16chain D and (resid 183:266 or resid 698:796)D183 - 266
50X-RAY DIFFRACTION16chain D and (resid 183:266 or resid 698:796)D698 - 796
51X-RAY DIFFRACTION17chain E and (resid 183:266 or resid 698:796)E183 - 266
52X-RAY DIFFRACTION17chain E and (resid 183:266 or resid 698:796)E698 - 796
53X-RAY DIFFRACTION18chain F and (resid 183:266 or resid 698:796)F183 - 266
54X-RAY DIFFRACTION18chain F and (resid 183:266 or resid 698:796)F698 - 796

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