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- PDB-3ow7: Crystal structure of the membrane fusion protein CusB from Escher... -

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Basic information

Entry
Database: PDB / ID: 3ow7
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
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 export / copper ion transmembrane transporter activity / 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 export / copper ion transmembrane transporter activity / 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 ...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
COPPER (I) ION / Cation efflux system protein CusB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.78 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 17, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 17, 2010ID: 3H9T
Revision 1.0Nov 17, 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 / 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_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_asym_id / _struct_conn.ptnr2_auth_seq_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)90,6136
Polymers90,3592
Non-polymers2544
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-50 kcal/mol
Surface area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.237, 111.008, 258.867
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
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu

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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: 3.35 Å3/Da / Density % sol: 63.27 %
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: 1.3779 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
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: 3.78→50 Å / Num. all: 12925 / Num. obs: 21143 / % possible obs: 96.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Χ2: 1.45 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.78-4.033.40.46723100.79284.9
4.03-4.243.40.33325000.86892.3
4.24-4.53.50.23926760.93497.5
4.5-4.853.70.17427311.29799.5
4.85-5.343.80.13227231.481100
5.34-6.113.80.12327491.535100
6.11-7.693.80.09227352.0499.9
7.69-503.70.04227192.31399.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.78→36.63 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3235 523 4.75 %RANDOM
Rwork0.2803 ---
obs0.2822 11008 82.84 %-
all-12925 --
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 188.444 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 584.59 Å2 / Biso mean: 227.7626 Å2 / Biso min: 126.92 Å2
Baniso -1Baniso -2Baniso -3
1--37.906 Å20 Å2-0 Å2
2--123.0981 Å20 Å2
3----85.1921 Å2
Refinement stepCycle: LAST / Resolution: 3.78→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 4 0 4545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064619
X-RAY DIFFRACTIONf_angle_d1.1886294
X-RAY DIFFRACTIONf_chiral_restr0.072760
X-RAY DIFFRACTIONf_plane_restr0.006807
X-RAY DIFFRACTIONf_dihedral_angle_d19.5051694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.78-4.07990.3803850.3311728181356
4.0799-4.66930.34551380.27972570270883
4.6693-5.87890.29461510.24352939309094
5.8789-36.63210.29821490.26543248339799

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