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- PDB-3h94: Crystal structure of the membrane fusion protein CusB from Escher... -

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Basic information

Entry
Database: PDB / ID: 3h94
TitleCrystal structure of the membrane fusion protein CusB from Escherichia coli
ComponentsCation efflux system protein cusB
KeywordsTRANSPORT PROTEIN / membrane fusion protein / CusCFBA copper/silver efflux system / Copper / Copper transport / Ion transport / Transport
Function / homology
Function and homology information


plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / transition metal ion binding ...plasma membrane copper ion transport / copper ion transmembrane transport / response to silver ion / silver ion transmembrane transport / cell envelope / copper ion transmembrane transporter activity / copper ion export / detoxification of copper ion / response to copper ion / transition metal ion binding / intracellular copper ion homeostasis / response to toxic substance / outer membrane-bounded periplasmic space / copper ion binding / membrane
Similarity search - Function
Helix Hairpins - #730 / Long alpha hairpin domain of cation efflux system protein, CusB / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Heavy metal binding domain / Heavy metal binding domain / 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 ...Helix Hairpins - #730 / Long alpha hairpin domain of cation efflux system protein, CusB / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Heavy metal binding domain / Heavy metal binding domain / 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 / Helix Hairpins / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SILVER ION / Cation efflux system protein CusB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.84 Å
AuthorsSu, C.-C. / Yang, F. / Long, F. / Reyon, D. / Routh, M.D. / Kuo, D.W. / Mokhtari, A.K. / Van Ornam, J.D. / Rabe, K.L. / Hoy, J.A. ...Su, C.-C. / Yang, F. / Long, F. / Reyon, D. / Routh, M.D. / Kuo, D.W. / Mokhtari, A.K. / Van Ornam, J.D. / Rabe, K.L. / Hoy, J.A. / Lee, Y.J. / Rajashankar, K.R. / Yu, E.W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the membrane fusion protein CusB from Escherichia coli
Authors: Su, C.C. / Yang, F. / Long, F. / Reyon, D. / Routh, M.D. / Kuo, D.W. / Mokhtari, A.K. / Van Ornam, J.D. / Rabe, K.L. / Hoy, J.A. / Lee, Y.J. / Rajashankar, K.R. / Yu, E.W.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cation efflux system protein cusB
B: Cation efflux system protein cusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9174
Polymers88,7012
Non-polymers2162
Water00
1
A: Cation efflux system protein cusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4592
Polymers44,3511
Non-polymers1081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cation efflux system protein cusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4592
Polymers44,3511
Non-polymers1081
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.005, 114.418, 259.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 95:102 or resseq 320:385 )
211chain B and (resseq 95:102 or resseq 320:385 )
112chain A and (resseq 103:119 or resseq 243:319 )
212chain B and (resseq 103:119 or resseq 243:319 )
113chain A and (resseq 154:206 )
213chain B and (resseq 154:206 )
114chain A and (resseq 120:153 or resseq 207:241 )
214chain B and (resseq 120:153 or resseq 207:241 )

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Cation efflux system protein cusB


Mass: 44350.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cusB, ylcD, b0574, JW0563 / Production host: Escherichia coli (E. coli) / References: UniProt: P77239
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 15%PEG1000, 360mM Lithium Citrate, 5% Glycerol, 5% Isopropanol, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.3779,0.9792,0.9793,0.9949
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.37791
20.97921
30.97931
40.99491
ReflectionResolution: 3.84→40 Å / Num. obs: 363533 / % possible obs: 99.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 24
Reflection shellResolution: 3.84→3.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 7.5 / % possible all: 95.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.84→47.2 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0.18 / Phase error: 36.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3 649 4.96 %
Rwork0.28 --
obs0.28 13089 87.3 %
all-14447 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 175.778 Å2
Baniso -1Baniso -2Baniso -3
1--2.8217 Å20 Å2-0 Å2
2--103.8426 Å20 Å2
3----43.2305 Å2
Refinement stepCycle: LAST / Resolution: 3.84→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 2 0 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014575
X-RAY DIFFRACTIONf_angle_d1.96233
X-RAY DIFFRACTIONf_dihedral_angle_d22.6981673
X-RAY DIFFRACTIONf_chiral_restr0.183754
X-RAY DIFFRACTIONf_plane_restr0.015798
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A544X-RAY DIFFRACTIONPOSITIONAL
12B544X-RAY DIFFRACTIONPOSITIONAL0.798
21A739X-RAY DIFFRACTIONPOSITIONAL
22B739X-RAY DIFFRACTIONPOSITIONAL0.862
31A417X-RAY DIFFRACTIONPOSITIONAL
32B417X-RAY DIFFRACTIONPOSITIONAL0.764
41A522X-RAY DIFFRACTIONPOSITIONAL
42B522X-RAY DIFFRACTIONPOSITIONAL0.802
Refinement TLS params.Method: refined / Origin x: 35.3115 Å / Origin y: 29.2141 Å / Origin z: 77.5602 Å
111213212223313233
T0.7809 Å20.0799 Å2-0.0711 Å2-0.4225 Å20.1707 Å2--0.8327 Å2
L0.8554 °20.0409 °20.0912 °2-0.0053 °2-0.3027 °2--0.0627 °2
S0.0603 Å °0.1864 Å °0.1041 Å °0.0376 Å °0.0358 Å °0.2292 Å °0.0488 Å °-0.2254 Å °-0.1049 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA89 - 385
2X-RAY DIFFRACTION1allB89 - 385
3X-RAY DIFFRACTION1allB - A1 - 408

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