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- PDB-8ytq: The structure of apoCopC from Thioalkalivibrio paradoxus -

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Basic information

Entry
Database: PDB / ID: 8ytq
TitleThe structure of apoCopC from Thioalkalivibrio paradoxus
ComponentsCopC domain-containing protein
KeywordsMETAL BINDING PROTEIN / CopC / Copper resistance protein C / Apo-form / Copper chaperone / Thioalkalivibrio paradoxus
Function / homology
Function and homology information


response to copper ion / periplasmic space / copper ion binding
Similarity search - Function
CopC domain / CopC domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / CopC domain-containing protein
Similarity search - Component
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKulikova, O.G. / Solovieva, A.Y. / Varfolomeeva, L.A. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of apoCopC from Thioalkalivibrio paradoxus
Authors: Kulikova, O.G. / Solovieva, A.Y. / Varfolomeeva, L.A. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.
History
DepositionMar 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CopC domain-containing protein
B: CopC domain-containing protein
C: CopC domain-containing protein
D: CopC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,64611
Polymers56,1464
Non-polymers5017
Water3,351186
1
A: CopC domain-containing protein
B: CopC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2915
Polymers28,0732
Non-polymers2193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-30 kcal/mol
Surface area12480 Å2
MethodPISA
2
C: CopC domain-containing protein
D: CopC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3556
Polymers28,0732
Non-polymers2824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-41 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.084, 144.787, 55.350
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
CopC domain-containing protein


Mass: 14036.403 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: THITH_13340 / Production host: Escherichia coli (E. coli) / References: UniProt: W0DSL1
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→55.35 Å / Num. obs: 47498 / % possible obs: 98.2 % / Redundancy: 4.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.048 / Rrim(I) all: 0.099 / Χ2: 0.93 / Net I/σ(I): 7.7 / Num. measured all: 194184
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 95.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.612 / Num. measured all: 10364 / Num. unique obs: 2495 / CC1/2: 0.814 / Rpim(I) all: 0.336 / Rrim(I) all: 0.7 / Χ2: 0.9 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.562 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23063 2376 5 %RANDOM
Rwork0.18413 ---
obs0.18644 45069 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.157 Å2
Baniso -1Baniso -2Baniso -3
1-9.67 Å20 Å2-5.17 Å2
2---13.59 Å2-0 Å2
3---3.91 Å2
Refinement stepCycle: 1 / Resolution: 1.7→55.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 21 186 4041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0123953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.6255391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92621.542214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08215564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8771530
X-RAY DIFFRACTIONr_chiral_restr0.1490.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0122.0022034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8212.9962533
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2682.3691919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.50229.3375707
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35860.11
12B35860.11
21A36480.12
22C36480.12
31A35690.12
32D35690.12
41B35310.12
42C35310.12
51B36320.09
52D36320.09
61C34950.12
62D34950.12
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.289 148 -
Rwork0.176 3168 -
obs--91.05 %

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