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- PDB-3lnn: Crystal structure of ZneB from Cupriavidus metallidurans -

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Basic information

Entry
Database: PDB / ID: 3lnn
TitleCrystal structure of ZneB from Cupriavidus metallidurans
ComponentsMembrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)Lipid bilayer fusion
KeywordsMETAL TRANSPORT / membrane fusion protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / MEMBRANE PROTEIN
Function / homology
Function and homology information


transmembrane transporter activity / membrane => GO:0016020 / metal ion binding
Similarity search - Function
conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain ...conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Membrane fusion protein (MFP-RND) heavy metal cation tricomponent efflux HmxB (CzcB-like)
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.796 Å
AuthorsLee, J.K. / De Angelis, F. / Miercke, L.J. / Stroud, R.M. / Vandenbussche, G. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems.
Authors: De Angelis, F. / Lee, J.K. / O'Connell, J.D. / Miercke, L.J. / Verschueren, K.H. / Srinivasan, V. / Bauvois, C. / Govaerts, C. / Robbins, R.A. / Ruysschaert, J.M. / Stroud, R.M. / Vandenbussche, G.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: 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_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_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.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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6573
Polymers77,5922
Non-polymers651
Water28816
1
A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8612
Polymers38,7961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)


Theoretical massNumber of molelcules
Total (without water)38,7961
Polymers38,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,3156
Polymers155,1844
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area9640 Å2
ΔGint-103 kcal/mol
Surface area57460 Å2
MethodPISA
4
A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,62912
Polymers310,3688
Non-polymers2624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area26470 Å2
ΔGint-235 kcal/mol
Surface area107740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.111, 137.111, 202.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like) / Lipid bilayer fusion / Secretion protein HlyD


Mass: 38795.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: Rmet_5330, ZneB / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1LCD7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Na-Acetate pH 5.4 1.9M Na-formate 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9796
SYNCHROTRONESRF ID23-121.0762
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 28, 2009Double crystal Si(111)
ADSC QUANTUM 3152CCDMay 19, 2009Single Si(111)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
21.07621
ReflectionResolution: 2.796→32.959 Å / Num. all: 23803 / Num. obs: 20621 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 72.76 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.074 / Net I/σ(I): 21
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 2360 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.796→32.959 Å / SU ML: 0.48 / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3135 1058 5.13 %RANDOM
Rwork0.2374 ---
obs0.2413 20621 85.07 %-
all-23803 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.18 Å2 / ksol: 0.294 e/Å3
Refinement stepCycle: LAST / Resolution: 2.796→32.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 1 16 4361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014516
X-RAY DIFFRACTIONf_angle_d1.7386140
X-RAY DIFFRACTIONf_dihedral_angle_d23.2631634
X-RAY DIFFRACTIONf_chiral_restr0.123706
X-RAY DIFFRACTIONf_plane_restr0.007828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.7964-2.92360.48771040.353720740.4877207473
2.9236-3.07770.39471200.318822490.3947224980
3.0777-3.27030.40121500.276123640.4012236484
3.2703-3.52260.37311320.278424030.3731240385
3.5226-3.87660.37421250.26223460.3742234682
3.8766-4.43640.27221430.1926140.2722261491
4.4364-5.58490.23441450.168527140.2344271494
5.5849-32.96080.28121390.232727990.2812279992
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.45970.3714-1.87251.1086-1.8241.3484-0.0253-0.0795-0.4326-0.99080.46620.08290.05570.7886-0.02870.8271-0.03850.22360.6863-0.08650.796422.4275-9.942634.9247
20.26990.6430.07581.0799-0.5671.7107-0.1974-0.05050.7826-1.00540.16911.1298-1.40590.60660.02520.37340.19070.0340.6785-0.11210.7569
30.73461.1379-0.65921.1081-0.91581.78620.00340.4437-0.18240.02760.32910.25840.5027-0.1252-0.10650.51630.0244-0.03030.3651-0.04170.3226
43.3263-0.5103-0.50670.92091.36181.4892-1.0637-0.4962-0.08280.23310.4405-0.0395-0.1399-0.16760.27280.445-0.06350.03370.35680.28120.2148
50.8995-0.7820.53421.146-0.23781.45130.4892-0.8101-0.0113-0.1243-0.00060.170.1158-0.1076-0.24330.5947-0.0373-0.10310.5270.0280.6465
61.341-0.3109-0.83841.41660.65081.94750.41070.0417-0.1397-0.14970.1559-0.3145-0.06840.1272-0.24050.35290.048-0.04850.4669-0.18570.5891
70.0173-0.0415-0.05461.7386-2.88533.605-0.0260.5061-0.18930.27090.37720.2523-0.966-0.0386-0.20850.7622-0.04280.29730.4161-0.05950.6463
80.6736-0.0164-0.45450.95720.78860.50870.04030.67981.7283-0.08761.7111-0.53680.4224-0.6551-0.19471.08620.113-0.07510.5022-0.05911.0201
9-0.0085-0.1052-0.35271.10430.12830.65990.2434-0.0260.33730.40090.0842-0.34360.10930.13740.06880.7490.09590.21710.47440.09110.7503
101.9293-0.77481.14681.02180.62080.75560.3477-0.4623-0.57190.08570.29640.01790.3913-0.0866-0.39660.67620.05650.01920.5930.2380.5703
111.05770.6682-0.41991.25-0.31430.67390.66-0.4245-0.0705-0.07-0.3550.3498-0.090.3103-0.21290.6955-0.09330.00750.57920.0780.6163
120.8899-1.8001-0.28711.3704-0.49513.80970.2013-0.12940.02530.17420.1694-0.12290.48820.678-0.22480.582-0.0828-0.12090.627-0.01320.6151
Refinement TLS groupSelection details: chain B and resid 205:281)

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