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- PDB-7z3b: Crystal structure of the cupredoxin AcoP from Acidithiobacillus f... -

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Basic information

Entry
Database: PDB / ID: 7z3b
TitleCrystal structure of the cupredoxin AcoP from Acidithiobacillus ferrooxidans, reduced form
ComponentsAcoP
KeywordsMETAL BINDING PROTEIN / cupredoxin / copper-binding
Function / homologyCupredoxin / metal ion binding / ACETATE ION / COPPER (I) ION / EfeO-type cupredoxin-like domain-containing protein
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsLeone, P. / Sciara, G. / Ilbert, M.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Dalton Trans / Year: 2024
Title: Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features.
Authors: Roger, M. / Leone, P. / Blackburn, N.J. / Horrell, S. / Chicano, T.M. / Biaso, F. / Giudici-Orticoni, M.T. / Abriata, L.A. / Hura, G.L. / Hough, M.A. / Sciara, G. / Ilbert, M.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AcoP
B: AcoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7329
Polymers38,2112
Non-polymers5217
Water3,117173
1
A: AcoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4125
Polymers19,1051
Non-polymers3074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AcoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3204
Polymers19,1051
Non-polymers2153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.951, 72.951, 112.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 43 - 181 / Label seq-ID: 31 - 169

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

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Components

#1: Protein AcoP


Mass: 19105.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria)
Gene: DN052_11965 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2W1KFF4
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM potassium acetate, 10mM potassium chloride, 50mM MES, 50mM Tris, 50mM Hepes, 34-44% PEG3000
PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07137 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07137 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 37412 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 15.4
Reflection shellResolution: 1.65→1.74 Å / Num. unique obs: 5387 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→44.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.7 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 1861 5 %RANDOM
Rwork0.1585 ---
obs0.16 35493 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.45 Å2 / Biso mean: 33.374 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.65→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 28 173 2317
Biso mean--43.69 40.97 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132355
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162122
X-RAY DIFFRACTIONr_angle_refined_deg1.931.6413215
X-RAY DIFFRACTIONr_angle_other_deg1.6261.584923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0825302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93423.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66615360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.771157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022743
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02579
Refine LS restraints NCS

Ens-ID: 1 / Number: 4165 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 119 -
Rwork0.268 2605 -
all-2724 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17930.0376-0.34531.049-0.06342.0979-0.0165-0.0454-0.01720.01660.0413-0.05620.11540.199-0.02480.02290.0310.01670.05880.01880.0266-28.255411.4129-9.4675
21.3074-0.26360.3172.9874-0.60331.69240.14110.0731-0.2992-0.2901-0.06240.36830.343-0.1176-0.07870.1128-0.0208-0.06460.0607-0.00430.1357-56.2999-1.7835-12.4001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 181
2X-RAY DIFFRACTION2B43 - 181

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