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

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Basic information

Entry
Database: PDB / ID: 3ooc
TitleCrystal structure of the membrane fusion protein CusB from Escherichia coli
ComponentsCation efflux system protein cusB
KeywordsTRANSPORT PROTEIN / three-helix bundle / BETA BARREL / Copper transport / Ion transport / Transport / CusA / CusC
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
Cation efflux system protein CusB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.404 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
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionDec 29, 2010ID: 3H9I
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)90,3592
Polymers90,3592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-11 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.962, 113.244, 258.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cation efflux system protein cusB / Membrane fusion protein


Mass: 45179.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cusB, ylcD, b0574, JW0563 / Production host: Escherichia coli (E. coli) / References: UniProt: P77239

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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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15%PEG1000, 360mM Lithium Citrate, 5% Glycerol, 5% Isopropanol, , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 19.74 / Number: 142012 / Rmerge(I) obs: 0.089 / Χ2: 1.81 / D res high: 3.83 Å / D res low: 50 Å / Num. obs: 23433 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.655099.410.0442.5775.7
6.087.6599.610.0782.0896
5.316.0899.610.1051.8466.1
4.825.3199.710.1181.9646.1
4.484.8299.710.1491.7926.2
4.224.4899.710.2121.5736.2
44.2299.610.311.4086.2
3.83499.310.4281.3346.1
ReflectionResolution: 3.44→50 Å / Num. all: 49228 / Num. obs: 30339 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 1.6 % / Rmerge(I) obs: 0.046 / Χ2: 1.414 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.44-3.61.60.38836990.88792.2
3.6-3.791.60.2839280.91998.3
3.79-4.021.60.16639461.06198.4
4.02-4.331.60.139291.12997.4
4.33-4.771.60.06638531.5396.7
4.77-5.461.60.05537721.75894.2
5.46-6.871.60.04836941.85992.4
6.87-501.70.03235182.09587.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 3.404→47.097 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3183 788 5.03 %
Rwork0.2609 --
obs0.2636 15676 89.27 %
all-15676 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 496.71 Å2 / Biso mean: 189.5188 Å2 / Biso min: 130.38 Å2
Baniso -1Baniso -2Baniso -3
1--23.4702 Å20 Å2-0 Å2
2--74.0711 Å20 Å2
3----50.6009 Å2
Refinement stepCycle: LAST / Resolution: 3.404→47.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 0 0 4548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044626
X-RAY DIFFRACTIONf_angle_d0.8836304
X-RAY DIFFRACTIONf_chiral_restr0.06762
X-RAY DIFFRACTIONf_plane_restr0.006808
X-RAY DIFFRACTIONf_dihedral_angle_d17.9981696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4036-3.61680.39071200.31322091221178
3.6168-3.89590.36151290.26282320244985
3.8959-4.28770.25291130.21572403251687
4.2877-4.90760.22221370.18812608274594
4.9076-6.18080.31791510.20842687283896
6.1808-47.10160.33271380.2662779291795
Refinement TLS params.Method: refined / Origin x: 35.2974 Å / Origin y: 29.0259 Å / Origin z: 77.3769 Å
111213212223313233
T1.9084 Å20.1707 Å2-0.0407 Å2-1.3855 Å20.112 Å2--1.7334 Å2
L0.7365 °20.1118 °2-0.3311 °2--0.2164 °2-0.346 °2---0.239 °2
S-0.0049 Å °0.1623 Å °-0.0113 Å °0.0454 Å °0.0007 Å °0.243 Å °-0.066 Å °-0.0584 Å °-0.0869 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA89 - 385
2X-RAY DIFFRACTION1allB89 - 385

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