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- PDB-7vw1: Structure of a dimeric periplasmic protein bound with cuprous ions -

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Basic information

Entry
Database: PDB / ID: 7vw1
TitleStructure of a dimeric periplasmic protein bound with cuprous 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 (I) ION / DUF305 domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.494 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0937
Polymers21,7752
Non-polymers3185
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-79 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.415, 77.415, 44.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 32 through 115 or (resid 116...
21(chain B and resid 32 through 116)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 32 through 115 or (resid 116...A0
211(chain B and resid 32 through 116)B32 - 116

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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-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.1 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Lithium chloride, 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: 2.494→50 Å / Num. obs: 9526 / % possible obs: 99.9 % / Redundancy: 19.3 % / Biso Wilson estimate: 39.39 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.049 / Net I/σ(I): 19.3
Reflection shellResolution: 2.494→2.59 Å / Rmerge(I) obs: 0.905 / Num. unique obs: 930 / CC1/2: 0.956 / Rpim(I) all: 0.309

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Processing

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

5ffb


Resolution: 2.494→34.621 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 388 4.81 %
Rwork0.203 7683 -
obs0.2052 8071 85.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.37 Å2 / Biso mean: 52.2696 Å2 / Biso min: 30.33 Å2
Refinement stepCycle: final / Resolution: 2.494→34.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 5 38 1418
Biso mean--57.77 48.15 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041396
X-RAY DIFFRACTIONf_angle_d0.6811855
X-RAY DIFFRACTIONf_chiral_restr0.038187
X-RAY DIFFRACTIONf_plane_restr0.004243
X-RAY DIFFRACTIONf_dihedral_angle_d15.923883
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A796X-RAY DIFFRACTION10.137TORSIONAL
12B796X-RAY DIFFRACTION10.137TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.494-2.85440.3573890.2806165556
2.8544-3.59560.25121160.23123025100
3.5956-34.6210.22611830.1721300399
Refinement TLS params.Method: refined / Origin x: 1.435 Å / Origin y: 23.7456 Å / Origin z: -3.4004 Å
111213212223313233
T0.7594 Å20.0717 Å20.0696 Å2-0.1508 Å20.0199 Å2--0.3372 Å2
L1.159 °2-0.0705 °20.8054 °2-1.372 °20.1773 °2--1.7114 °2
S0.119 Å °-0.1297 Å °-0.0268 Å °0.2015 Å °0.0349 Å °0.0574 Å °0.3675 Å °0.0621 Å °-0.1094 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 116
2X-RAY DIFFRACTION1allB25 - 116
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allC3 - 4
5X-RAY DIFFRACTION1allC5
6X-RAY DIFFRACTION1allS1 - 39

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