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- PDB-6fan: Crystal structure of putative CooT from Carboxydothermus hydrogen... -

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Basic information

Entry
Database: PDB / ID: 6fan
TitleCrystal structure of putative CooT from Carboxydothermus hydrogenoformans
ComponentsCooT
KeywordsMETAL BINDING PROTEIN / Carbon monoxide dehydrogenase / nickel chaperone / maturation pathway
Function / homologyCO dehydrogenase accessory protein CooT / CO dehydrogenase accessory protein CooT / Uncharacterized protein
Function and homology information
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCavazza, C. / Alfano, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2018
Title: Biophysical and structural characterization of the putative nickel chaperone CooT from Carboxydothermus hydrogenoformans.
Authors: Alfano, M. / Perard, J. / Miras, R. / Catty, P. / Cavazza, C.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CooT
B: CooT
C: CooT
D: CooT
E: CooT
F: CooT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66214
Polymers43,8216
Non-polymers8418
Water1,08160
1
E: CooT
hetero molecules

A: CooT


Theoretical massNumber of molelcules
Total (without water)14,9095
Polymers14,6072
Non-polymers3023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_346-x-2,y-1/2,-z+11
2
A: CooT

E: CooT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9095
Polymers14,6072
Non-polymers3023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_356-x-2,y+1/2,-z+11
Buried area1680 Å2
ΔGint-14 kcal/mol
Surface area7050 Å2
MethodPISA
3
B: CooT
F: CooT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9095
Polymers14,6072
Non-polymers3023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area6940 Å2
MethodPISA
4
C: CooT
D: CooT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8434
Polymers14,6072
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.261, 61.350, 81.118
Angle α, β, γ (deg.)90.00, 100.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 62
2010B2 - 62
1020A2 - 61
2020C2 - 61
1030A2 - 61
2030D2 - 61
1040A2 - 62
2040E2 - 62
1050A2 - 61
2050F2 - 61
1060B2 - 61
2060C2 - 61
1070B2 - 61
2070D2 - 61
1080B2 - 62
2080E2 - 62
1090B2 - 61
2090F2 - 61
10100C2 - 61
20100D2 - 61
10110C2 - 61
20110E2 - 61
10120C2 - 61
20120F2 - 61
10130D2 - 61
20130E2 - 61
10140D1 - 62
20140F1 - 62
10150E2 - 61
20150F2 - 61

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
CooT


Mass: 7303.479 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria)
Gene: CHY_0178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3AFN4
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 47% (v/v) 2-methylpentane-2,4-diol, 2% (v/v) 2-methyl-2-propanol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97979 Å / Relative weight: 1
ReflectionResolution: 2→33.85 Å / Num. obs: 97738 / % possible obs: 97.6 % / Redundancy: 1.9 % / Net I/σ(I): 13.41
Reflection shellResolution: 2→2.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→79.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.304 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27517 1299 4.9 %RANDOM
Rwork0.23463 ---
obs0.23658 25451 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-2.65 Å2
2--2.4 Å20 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 2→79.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 55 60 3052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0962.0194096
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87123.986143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83915625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.651532
X-RAY DIFFRACTIONr_chiral_restr0.1360.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022169
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_it5.084.6781483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.8636.9781846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7565.011577
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.76587.18311005
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)
11A33600.08
12B33600.08
21A33100.07
22C33100.07
31A32180.1
32D32180.1
41A33400.1
42E33400.1
51A32500.1
52F32500.1
61B34300.08
62C34300.08
71B32380.11
72D32380.11
81B34300.1
82E34300.1
91B32840.1
92F32840.1
101C31280.1
102D31280.1
111C32480.12
112E32480.12
121C31560.11
122F31560.11
131D32720.1
132E32720.1
141D33620.1
142F33620.1
151E33220.1
152F33220.1
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 97 -
Rwork0.37 1886 -
obs--98.31 %

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