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- PDB-6hk5: X-ray structure of a truncated mutant of the metallochaperone Coo... -

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Basic information

Entry
Database: PDB / ID: 6hk5
TitleX-ray structure of a truncated mutant of the metallochaperone CooJ with a high-affinity nickel-binding site
ComponentsCooJ
KeywordsMETAL BINDING PROTEIN / metallochaperone / nickel-binding
Function / homologyNICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3,3',3''-phosphoryltripropanoic acid / CooJ
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.042 Å
AuthorsAlfano, M. / Perard, J. / Basset, C. / Carpentier, P. / Zambelli, B. / Timm, J. / Crouzy, S. / Ciurli, S. / Cavazza, C.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The carbon monoxide dehydrogenase accessory protein CooJ is a histidine-rich multidomain dimer containing an unexpected Ni(II)-binding site.
Authors: Alfano, M. / Perard, J. / Carpentier, P. / Basset, C. / Zambelli, B. / Timm, J. / Crouzy, S. / Ciurli, S. / Cavazza, C.
History
DepositionSep 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CooJ
C: CooJ
E: CooJ
G: CooJ
A: CooJ
D: CooJ
F: CooJ
H: CooJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,07222
Polymers60,8508
Non-polymers1,22214
Water5,405300
1
B: CooJ
C: CooJ
E: CooJ
G: CooJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,79511
Polymers30,4254
Non-polymers3707
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-118 kcal/mol
Surface area12450 Å2
MethodPISA
2
B: CooJ
C: CooJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5829
Polymers15,2122
Non-polymers3707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-59 kcal/mol
Surface area6980 Å2
MethodPISA
3
E: CooJ
G: CooJ


Theoretical massNumber of molelcules
Total (without water)15,2122
Polymers15,2122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-43 kcal/mol
Surface area7060 Å2
MethodPISA
4
A: CooJ
D: CooJ
F: CooJ
H: CooJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,27711
Polymers30,4254
Non-polymers8527
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-64 kcal/mol
Surface area12260 Å2
MethodPISA
5
A: CooJ
D: CooJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0659
Polymers15,2122
Non-polymers8527
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-23 kcal/mol
Surface area7200 Å2
MethodPISA
6
F: CooJ
H: CooJ


Theoretical massNumber of molelcules
Total (without water)15,2122
Polymers15,2122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-34 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 74.280, 70.640
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules BCEGADFH

#1: Protein
CooJ


Mass: 7606.244 Da / Num. of mol.: 8 / Fragment: Residues 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: cooJ / Plasmid: pET15b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P72321

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Non-polymers , 7 types, 314 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-Z3P / 3,3',3''-phosphoryltripropanoic acid


Mass: 266.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O7P
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein concentration of 10 mgmL-1 and 1 equivalent of Ni(II) per dimer, crystals were grown in 16% PEG3350 and 0.2 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.04→46.746 Å / Num. obs: 30586 / % possible obs: 99.2 % / Observed criterion σ(I): 1.5 / Redundancy: 6.4 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.14 / Net I/σ(I): 9.4
Reflection shellResolution: 2.04→2.16 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 4749 / CC1/2: 0.691 / Rrim(I) all: 0.88 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.042→46.746 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.2585 1409 4.61 %
Rwork0.1996 --
obs0.2024 30586 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.042→46.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 63 300 4131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073885
X-RAY DIFFRACTIONf_angle_d15214
X-RAY DIFFRACTIONf_dihedral_angle_d15.1522348
X-RAY DIFFRACTIONf_chiral_restr0.04594
X-RAY DIFFRACTIONf_plane_restr0.005690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0417-2.11470.38961230.29892768X-RAY DIFFRACTION95
2.1147-2.19930.30081320.24482919X-RAY DIFFRACTION100
2.1993-2.29940.28771560.22312922X-RAY DIFFRACTION100
2.2994-2.42070.31481400.20962917X-RAY DIFFRACTION100
2.4207-2.57230.2661560.20852910X-RAY DIFFRACTION100
2.5723-2.77090.27571310.20782951X-RAY DIFFRACTION100
2.7709-3.04970.29361470.20772908X-RAY DIFFRACTION100
3.0497-3.49090.23941490.19942932X-RAY DIFFRACTION100
3.4909-4.39760.24251390.16942962X-RAY DIFFRACTION100
4.3976-46.75870.21471360.18842988X-RAY DIFFRACTION99

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