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- PDB-7vw0: Structure of a dimeric periplasmic protein -

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Basic information

Entry
Database: PDB / ID: 7vw0
TitleStructure of a dimeric periplasmic protein
ComponentsDUF305 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Copper binding protein / Metal homeostasis
Function / homologyDomain of unknown function DUF305, CopM-like / Domain of unknown function (DUF305) / Ferritin-like / DUF305 domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.447 Å
AuthorsYang, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870729 China
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: Structural basis of copper binding by a dimeric periplasmic protein forming a six-helical bundle.
Authors: Yang, J. / Gao, M. / Wang, J. / He, C. / Wang, X. / Liu, L.
History
DepositionNov 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF305 domain-containing protein
B: DUF305 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)24,1802
Polymers24,1802
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-44 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.296, 73.242, 73.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DUF305 domain-containing protein


Mass: 12089.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: O2R_94 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6EME5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: MES, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.447→50 Å / Num. obs: 35568 / % possible obs: 97.3 % / Redundancy: 12.5 % / Biso Wilson estimate: 21.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Net I/σ(I): 21.5
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 3440 / CC1/2: 0.87 / Rpim(I) all: 0.328

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FFB

5ffb


Resolution: 1.447→20.435 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 1811 5.1 %
Rwork0.154 33708 -
obs0.1565 35519 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.79 Å2 / Biso mean: 36.4367 Å2 / Biso min: 18.31 Å2
Refinement stepCycle: final / Resolution: 1.447→20.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 197 1605
Biso mean---50.35 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071467
X-RAY DIFFRACTIONf_angle_d0.8211958
X-RAY DIFFRACTIONf_chiral_restr0.06196
X-RAY DIFFRACTIONf_plane_restr0.005259
X-RAY DIFFRACTIONf_dihedral_angle_d15.847574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.447-1.48570.29611190.2554242891
1.4857-1.52940.29681330.2211248396
1.5294-1.57880.2711130.206257396
1.5788-1.63520.19591260.1796253996
1.6352-1.70060.24861260.1662256997
1.7006-1.7780.21821540.1623255197
1.778-1.87170.22341260.153259797
1.8717-1.98880.20291790.1434252398
1.9888-2.14230.19341240.1437261898
2.1423-2.35760.19891560.1282264298
2.3576-2.6980.18841260.1422266799
2.698-3.39670.20311500.1552270599
3.3967-20.4350.17871790.1546281399

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