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- PDB-7vw2: Structure of a dimeric periplasmic protein bound with cupric ions -

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Basic information

Entry
Database: PDB / ID: 7vw2
TitleStructure of a dimeric periplasmic protein bound with cupric ions
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 / COPPER (II) ION / DUF305 domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.186 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,28310
Polymers21,7752
Non-polymers5088
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-80 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.446, 74.412, 50.786
Angle α, β, γ (deg.)90.000, 96.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

CU

21A-202-

CU

31B-201-

CU

41B-202-

CU

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 32 through 85 or resid 87 through 116))
21(chain B and (resid 32 through 85 or resid 87...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLY(chain A and (resid 32 through 85 or resid 87 through 116))AA32 - 8512 - 65
12ASPASPLYSLYS(chain A and (resid 32 through 85 or resid 87 through 116))AA87 - 11667 - 96
21SERSERGLYGLY(chain B and (resid 32 through 85 or resid 87...BB32 - 8512 - 65
22ASPASPLEULEU(chain B and (resid 32 through 85 or resid 87...BB87 - 11267 - 92
23ASPASPASPASP(chain B and (resid 32 through 85 or resid 87...BB11393
24SERSERLYSLYS(chain B and (resid 32 through 85 or resid 87...BB32 - 11612 - 96
25SERSERLYSLYS(chain B and (resid 32 through 85 or resid 87...BB32 - 11612 - 96
26SERSERLYSLYS(chain B and (resid 32 through 85 or resid 87...BB32 - 11612 - 96
27SERSERLYSLYS(chain B and (resid 32 through 85 or resid 87...BB32 - 11612 - 96

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Components

#1: Protein DUF305 domain-containing protein / Orf91


Mass: 10887.481 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: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Sodium thiocyanate, AmSO4

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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: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.186→50 Å / Num. obs: 9492 / % possible obs: 97.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.037 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 941 / CC1/2: 0.932 / Rpim(I) all: 0.237 / % possible all: 98.1

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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: 2.186→33.607 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2818 444 5.2 %
Rwork0.2452 8088 -
obs0.2472 8532 87.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.44 Å2 / Biso mean: 35.0359 Å2 / Biso min: 10.59 Å2
Refinement stepCycle: final / Resolution: 2.186→33.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 8 41 1360
Biso mean--62.6 23.88 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051338
X-RAY DIFFRACTIONf_angle_d0.6621780
X-RAY DIFFRACTIONf_chiral_restr0.039181
X-RAY DIFFRACTIONf_plane_restr0.004232
X-RAY DIFFRACTIONf_dihedral_angle_d21.123526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A771X-RAY DIFFRACTION15.676TORSIONAL
12B771X-RAY DIFFRACTION15.676TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1863-2.50260.35211080.2887208068
2.5026-3.15260.28581570.2606300498
3.1526-33.6070.26331790.2244300497
Refinement TLS params.Method: refined / Origin x: 6.1653 Å / Origin y: -8.759 Å / Origin z: 13.3145 Å
111213212223313233
T0.181 Å2-0.2306 Å2-0.0179 Å2-0.1811 Å20.0735 Å2--0.0886 Å2
L0.7993 °20.9713 °2-0.0246 °2-1.3852 °2-0.0075 °2--0.5178 °2
S0.1858 Å °-0.2327 Å °-0.132 Å °0.1682 Å °-0.0793 Å °-0.1342 Å °0.1486 Å °-0.0448 Å °0.0794 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 116
2X-RAY DIFFRACTION1allB32 - 116
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allC3 - 4
5X-RAY DIFFRACTION1allC5 - 8
6X-RAY DIFFRACTION1allS2 - 46

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