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- PDB-8r4m: CSP1 M48L mutant with Iodide -

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Basic information

Entry
Database: PDB / ID: 8r4m
TitleCSP1 M48L mutant with 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 / identical protein binding / COPPER (I) ION / IODIDE ION / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)24,39830
Polymers22,4922
Non-polymers1,90628
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-194 kcal/mol
Surface area11300 Å2
Unit cell
Length a, b, c (Å)87.744, 87.744, 50.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 15 - 122 / Label seq-ID: 2 - 109

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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

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Components

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


Mass: 11246.046 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Bicine pH 8.5 plus 12.5% v/v 2-methyl-2,4 pentanediol (racemic), 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 0.03 M sodium fluoride, 0.03 M sodium bromide and 0.03 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→43.9 Å / Num. obs: 14827 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rmerge(I) obsRpim(I) allRrim(I) all
8.94-43.8710.11981
1.95-213.510220.7931.7360.6951.872

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
Aimlessdata scaling
xia2data reduction
XDSdata reduction
MOLREPphasing
BUSTERrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.872 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.341 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / ESU R: 0.16 / ESU R Free: 0.153 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2297 715 4.847 %
Rwork0.1786 14036 -
all0.181 --
obs-14751 99.709 %
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: 46.818 Å2
Baniso -1Baniso -2Baniso -3
1--2.304 Å20 Å20 Å2
2---2.304 Å20 Å2
3---4.609 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 28 64 1579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121506
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6232028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7082552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54915250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.517152
X-RAY DIFFRACTIONr_chiral_restr0.1180.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021112
X-RAY DIFFRACTIONr_nbd_refined0.2330.2806
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.277
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.23
X-RAY DIFFRACTIONr_mcbond_it4.0184.434833
X-RAY DIFFRACTIONr_mcangle_it5.1446.6171036
X-RAY DIFFRACTIONr_scbond_it5.5444.891673
X-RAY DIFFRACTIONr_scangle_it7.5677.124992
X-RAY DIFFRACTIONr_lrange_it7.92362.7692381
X-RAY DIFFRACTIONr_ncsr_local_group_10.0920.052956
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.091510.05008
12BX-RAY DIFFRACTIONLocal ncs0.091510.05008
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
1.95-2.0010.311460.32110230.3210740.6320.55299.53450.311
2.001-2.0550.25450.39680.29810180.6870.65999.50880.283
2.055-2.1150.335520.2749610.27810170.7060.74599.60670.255
2.115-2.180.276440.2359460.2369970.7750.8299.29790.204
2.18-2.2510.24570.2198950.229580.8530.86999.37370.188
2.251-2.330.199440.1988600.1989090.9060.90999.44990.17
2.33-2.4170.229420.1928590.1949030.9150.92399.77850.161
2.417-2.5160.193400.1858350.1858780.9290.93399.65830.156
2.516-2.6270.262350.1847890.1878250.9170.9499.87880.157
2.627-2.7550.281380.1957560.1997940.9090.9351000.168
2.755-2.9030.25390.27320.2037710.8960.9361000.169
2.903-3.0790.201350.1876810.1887160.9520.9431000.164
3.079-3.290.234350.1626490.1666840.9440.9591000.143
3.29-3.5520.223330.1426120.1466450.9530.9681000.131
3.552-3.8890.163290.1485680.1495970.9640.9721000.137
3.889-4.3430.228320.1495060.1545380.9530.9711000.14
4.343-5.0070.24220.1434710.1464930.9350.9731000.138
5.007-6.1130.204260.1713900.1734160.9640.9631000.161
6.113-8.5620.199100.1343310.1353410.9580.981000.133
8.562-43.8720.263110.22030.2022180.9540.95398.16510.281

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