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- PDB-7z3f: Crystal structure of the cupredoxin AcoP from Acidithiobacillus f... -

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Basic information

Entry
Database: PDB / ID: 7z3f
TitleCrystal structure of the cupredoxin AcoP from Acidithiobacillus ferrooxidans, oxidized form
ComponentsAcoP
KeywordsMETAL BINDING PROTEIN / cupredoxin / copper-binding
Function / homologyCupredoxin / metal ion binding / ACETATE ION / COPPER (II) ION / EfeO-type cupredoxin-like domain-containing protein
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)38,87514
Polymers38,2112
Non-polymers66412
Water2,216123
1
A: AcoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5308
Polymers19,1051
Non-polymers4247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AcoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3456
Polymers19,1051
Non-polymers2405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.477, 73.477, 112.902
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: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 43 - 180 / Label seq-ID: 31 - 168

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

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 135 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.99 Å3/Da / Density % sol: 38.32 %
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: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 34624 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.987 / Net I/σ(I): 6.1
Reflection shellResolution: 1.7→1.79 Å / Num. unique obs: 4976 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Z3B

7z3b


Resolution: 1.7→38.26 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.511 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1688 4.9 %RANDOM
Rwork0.2364 ---
obs0.2375 32890 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.31 Å2 / Biso mean: 29.042 Å2 / Biso min: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0 Å2
2--0.14 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.7→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 34 123 2250
Biso mean--43.75 35.16 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132190
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161962
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6432970
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5784524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15623.063111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71415319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.944157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02536
Refine LS restraints NCS

Ens-ID: 1 / Number: 4002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 109 -
Rwork0.328 2396 -
all-2505 -
obs--99.72 %
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)
10.92260.2628-0.34080.6522-0.11161.7505-0.0242-0.0415-0.02660.01460.0202-0.03150.0360.110.0040.01990.02190.00650.03510.00930.00558.2827-25.2112-9.5791
20.8317-0.22910.01192.5552-0.49881.40610.0280.0624-0.109-0.25760.01090.29970.2498-0.2436-0.03890.0852-0.0419-0.0380.0939-00.0479-19.5253-38.5016-12.306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 181
2X-RAY DIFFRACTION2B43 - 180

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