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- PDB-9gsk: CSP1 H36A plus imidazole -

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Basic information

Entry
Database: PDB / ID: 9gsk
TitleCSP1 H36A plus imidazole
ComponentsCopper storage protein 1
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 / Protein of unknown function DUF326 / Copper storage protein / metal ion binding / COPPER (II) ION / COPPER (I) ION / IMIDAZOLE / Copper storage protein 1
Function and homology information
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.3 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
DepositionSep 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper storage protein 1
B: Copper storage protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,36231
Polymers22,5082
Non-polymers1,85429
Water2,198122
1
A: Copper storage protein 1
B: Copper storage protein 1
hetero molecules

A: Copper storage protein 1
B: Copper storage protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,72462
Polymers45,0164
Non-polymers3,70858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12660 Å2
ΔGint-426 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.42, 98.28, 83.43
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1014-

CU

21A-1155-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 13 - 122 / Label seq-ID: 1 - 110

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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

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Components

#1: Protein Copper storage protein 1


Mass: 11254.065 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Production host: Methylosinus trichosporium OB3b (bacteria) / References: UniProt: A0A0M3KL60
#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
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop
Details: 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM LFucose, 20 mM D-Xylose, 20 mM N-Acetyl-D-Glucosamine, 100 mM Imidazol/MES pH 6.5, 40% Glycerol and 20% PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→51.47 Å / Num. obs: 61289 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Χ2: 0.87 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
7.12-51.4710.10.02844.24320.9980.0120.0310.4499.6
1.3-1.3213.12.2321.230010.4860.9312.420.89100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
REFMAC5.8.0430 (refmacat 0.4.82)refinement
RefinementMethod to determine structure: MIR / Resolution: 1.3→51.47 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.789 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.042 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1806 3118 5.09 %
Rwork0.1709 58139 -
all0.171 --
obs-61257 99.982 %
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: 23.281 Å2
Baniso -1Baniso -2Baniso -3
1-0.893 Å20 Å2-0 Å2
2---0.427 Å20 Å2
3----0.466 Å2
Refinement stepCycle: LAST / Resolution: 1.3→51.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 37 122 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121647
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.8082231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2935238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.94852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59910275
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.641055
X-RAY DIFFRACTIONr_chiral_restr0.1260.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021228
X-RAY DIFFRACTIONr_nbd_refined0.2120.2854
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.286
X-RAY DIFFRACTIONr_metal_ion_refined0.2170.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1940.22
X-RAY DIFFRACTIONr_mcbond_it1.9892.043901
X-RAY DIFFRACTIONr_mcangle_it2.6973.6641129
X-RAY DIFFRACTIONr_scbond_it3.7572.428746
X-RAY DIFFRACTIONr_scangle_it5.2944.2751093
X-RAY DIFFRACTIONr_lrange_it4.98624.4692696
X-RAY DIFFRACTIONr_ncsr_local_group_10.0680.053367
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.067990.05008
12BX-RAY DIFFRACTIONLocal ncs0.067990.05008
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
1.3-1.3340.3262190.30242650.30344850.920.92899.97770.294
1.334-1.370.2892390.2841540.28143950.9370.94199.95450.267
1.37-1.410.2642250.25940260.2642530.9570.95499.9530.241
1.41-1.4530.232170.22938830.22941000.9660.9651000.206
1.453-1.5010.2092070.20237890.20239960.9740.9741000.179
1.501-1.5540.2011980.17836970.17938950.9730.981000.155
1.554-1.6120.1582000.15635580.15637580.9820.9851000.133
1.612-1.6780.1721880.14934030.1535910.9830.9861000.126
1.678-1.7520.171860.13932890.14134750.9840.9881000.119
1.752-1.8380.1871360.14131670.14333030.9790.9881000.125
1.838-1.9370.1751680.15430080.15531760.9820.9851000.14
1.937-2.0550.1821290.16228710.16330000.9780.9841000.156
2.055-2.1960.1841270.16326930.16428200.9790.9841000.162
2.196-2.3720.1591570.15124660.15226250.9830.98699.92380.158
2.372-2.5980.1621230.16723190.16724420.9820.9831000.18
2.598-2.9030.2241060.1920990.19122050.9730.9791000.212
2.903-3.3510.1841070.17918600.17919670.9790.981000.209
3.351-4.0990.146680.16116160.16116840.9860.9851000.194
4.099-5.7790.188800.16312350.16413150.980.9841000.205
5.779-51.470.127380.1647410.1637830.990.97999.48910.217

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