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- PDB-8r4l: CSP1 M48L mutant without Iodide -

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Basic information

Entry
Database: PDB / ID: 8r4l
TitleCSP1 M48L mutant without Iodide
ComponentsFour-helix bundle copper-binding protein
KeywordsMETAL BINDING PROTEIN / COPPER BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE
Function / homologyTwin-arginine translocation signal, Cys-rich four helix bundle protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / metal ion binding / identical protein binding / COPPER (II) ION / COPPER (I) ION / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasle, A. / David, S. / Dennison, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The replacement of a Met ligand by iodide in a copper storage protein is stabilised by an unusual Cu(I)2-anion-pi interaction
Authors: David, S. / Dalton, R.A. / Basle, A. / Crowley, P.B. / Dennison, C.
History
DepositionNov 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Four-helix bundle copper-binding protein
B: Four-helix bundle copper-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,89929
Polymers25,1832
Non-polymers1,71627
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-187 kcal/mol
Surface area12210 Å2
Unit cell
Length a, b, c (Å)94.579, 41.755, 53.739
Angle α, β, γ (deg.)90, 95.588, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1014-

CU

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 12 - 122 / Label seq-ID: 12 - 122

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Four-helix bundle copper-binding protein


Mass: 12591.491 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12740 / Production host: Methylosinus trichosporium OB3b (bacteria) / References: UniProt: A0A2D2D105
#2: Chemical...
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Bicine pH 8.5 plus 14% v/v 2-methyl-2,4 pentanediol (racemic), 14% w/v PEG 1000, 14% w/v PEG 3350, 0.03 M MgCl2 and 0.03 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→38.17 Å / Num. obs: 14161 / % possible obs: 99 % / Redundancy: 3.2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.108 / Rrim(I) all: 0.16 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
8.94-38.172.3141610.9821
2-2.052.710170.3281

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.168 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.954 / SU ML: 0.172 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2706 671 4.738 %
Rwork0.2202 13490 -
all0.223 --
obs-14161 98.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.092 Å2
Baniso -1Baniso -2Baniso -3
1-0.728 Å2-0 Å20.013 Å2
2---1.536 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2→38.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 27 32 1635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121598
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161488
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.812154
X-RAY DIFFRACTIONr_angle_other_deg0.5521.7523458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.95552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77510262
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.6161054
X-RAY DIFFRACTIONr_chiral_restr0.0830.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined0.2310.2392
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21133
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2824
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.243
X-RAY DIFFRACTIONr_metal_ion_refined0.2040.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.28
X-RAY DIFFRACTIONr_nbd_other0.1450.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.26
X-RAY DIFFRACTIONr_mcbond_it3.4713.601886
X-RAY DIFFRACTIONr_mcbond_other3.473.601886
X-RAY DIFFRACTIONr_mcangle_it5.3826.4581104
X-RAY DIFFRACTIONr_mcangle_other5.3826.4631105
X-RAY DIFFRACTIONr_scbond_it5.0474.307712
X-RAY DIFFRACTIONr_scbond_other5.0484.308712
X-RAY DIFFRACTIONr_scangle_it7.6937.6151050
X-RAY DIFFRACTIONr_scangle_other7.6897.6191051
X-RAY DIFFRACTIONr_lrange_it9.1533.9261858
X-RAY DIFFRACTIONr_lrange_other9.15533.3341854
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.053219
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.067230.05009
12AX-RAY DIFFRACTIONLocal ncs0.067230.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.595390.4939720.49810340.7490.82697.77560.342
2.052-2.1080.523520.4579480.46110220.7920.8297.84740.331
2.108-2.1690.332530.4019350.3979990.9170.86298.89890.296
2.169-2.2350.277400.3358950.3329550.9430.90997.90580.284
2.235-2.3080.341340.3048940.3059460.8690.90798.09730.246
2.308-2.3890.31310.2248520.2278870.9380.9699.5490.21
2.389-2.4790.273350.1868400.1898830.9640.97699.0940.19
2.479-2.580.274330.1898150.1928520.9560.97799.53050.194
2.58-2.6940.249320.1847740.1878080.9640.9899.75250.188
2.694-2.8250.229500.1657110.1697700.970.98398.83120.171
2.825-2.9760.194380.1567010.1587450.9790.98599.19460.169
2.976-3.1560.205250.1666620.1686940.9790.98298.99140.182
3.156-3.3720.249400.1566180.1626620.960.98399.39580.179
3.372-3.640.156350.1585600.1586040.9860.98498.50990.181
3.64-3.9840.217310.165470.1635800.970.98599.65520.182
3.984-4.4480.229280.1734850.1765140.9610.98399.80550.211
4.448-5.1240.251250.1744360.1774630.9520.98399.5680.219
5.124-6.2480.255210.1983690.2023910.9660.97699.74420.237
6.248-8.720.268180.173000.1753180.9590.9831000.226
8.72-38.1680.301110.211760.2161880.9810.97899.46810.286

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