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

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Basic information

Entry
Database: PDB / ID: 3opo
TitleCrystal structure of the membrane fusion protein CusB from Escherichia coli
ComponentsCation efflux system protein cusB
KeywordsTRANSPORT PROTEIN / 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
SILVER ION / Cation efflux system protein CusB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.848 Å
AuthorsSu, C.-C.
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
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: 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 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Cation efflux system protein cusB
B: Cation efflux system protein cusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5754
Polymers90,3592
Non-polymers2162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-25 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.803, 114.678, 259.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 K-12 (bacteria) / Strain: K12 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG1000 15%, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.3779 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3779 Å / Relative weight: 1
ReflectionResolution: 3.84→50 Å / Num. obs: 12345 / % possible obs: 99.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4
Reflection shellResolution: 3.84→3.98 Å / % possible all: 95.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.848→39.31 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.81 / σ(F): 0 / Phase error: 35.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3397 541 4.81 %
Rwork0.295 --
obs0.2971 11252 90.87 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 295.178 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--24.5912 Å20 Å2-0 Å2
2--91.3205 Å2-0 Å2
3----66.7292 Å2
Refinement stepCycle: LAST / Resolution: 3.848→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 2 0 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054619
X-RAY DIFFRACTIONf_angle_d0.9626294
X-RAY DIFFRACTIONf_dihedral_angle_d16.4071704
X-RAY DIFFRACTIONf_chiral_restr0.063760
X-RAY DIFFRACTIONf_plane_restr0.004807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8485-4.23540.3871180.36752205X-RAY DIFFRACTION76
4.2354-4.84730.34711300.27272644X-RAY DIFFRACTION92
4.8473-6.10340.35711400.29132836X-RAY DIFFRACTION96
6.1034-39.31190.32321530.29053026X-RAY DIFFRACTION99

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