PDB-7bk6: PfCopC mutant - D83A

ID or keywords:

Entry

Database: PDB / ID: 7bk6

Title

PfCopC mutant - D83A

Components

Putative copper resistance protein

Keywords

METAL BINDING PROTEIN / Copper binding / copper transport

Function / homology

Function and homology information

copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Muderspach, S.J. / Ipsen, J. / Rollan, C.H. / Bertelsen, A.B. / Norholm, M.H.H. / Johansen, K.S. / Lo Leggio, L.

Funding support

Denmark, 1items

Citation

Journal: Febs Lett. / Year: 2021
Title: Copper binding and reactivity at the histidine brace motif: insights from mutational analysis of the Pseudomonas fluorescens copper chaperone CopC.
Authors: Ipsen, J.O. / Hernandez-Rollan, C. / Muderspach, S.J. / Brander, S. / Bertelsen, A.B. / Jensen, P.E. / Norholm, M.H.H. / Lo Leggio, L. / Johansen, K.S.

History

Deposition	Jan 15, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7bk6.cif.gz	54.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7bk6.ent.gz		Display	PDB format
PDBx/mmJSON format	7bk6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7bk6_validation.pdf.gz	453.4 KB	Display	wwPDB validaton report
Full document	7bk6_full_validation.pdf.gz	458 KB	Display
Data in XML	7bk6_validation.xml.gz	11 KB	Display
Data in CIF	7bk6_validation.cif.gz	14.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bk/7bk6 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bk6	HTTPS FTP

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Related structure data

Related structure data	7bk5C 7bk7C 6nfqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6nfq-1 6nfq-3 7bk7-2 7bk6-2 7bk5-d 104d-d 6nfs-d 6tpb-d 2bx5-13 3r15-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Putative copper resistance protein

BBB: Putative copper resistance protein

hetero molecules

20.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Putative copper resistance protein

hetero molecules

defined by author
10.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Putative copper resistance protein

hetero molecules

defined by author
10.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.060, 80.060, 89.400
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	80
Space group name H-M	I4₁

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Protein , 1 types, 2 molecules AAABBB

#1: Protein	Putative copper resistance protein Mass: 10066.284 Da / Num. of mol.: 2 / Mutation: D83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SBW25 / Gene: PFLU_3946 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C3JYL7

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Non-polymers , 6 types, 93 molecules

#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.56 Å³/Da / Density % sol: 65.43 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.5 M ammonium sulphate, 0.1 M sodium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.15→44.7 Å / Num. obs: 15379 / % possible obs: 100 % / Redundancy: 13.7 % / CC_1/2: 1 / Net I/σ(I): 18.69
Reflection shell	Resolution: 2.15→2.21 Å / Redundancy: 13 % / Num. unique obs: 1136 / CC_1/2: 0.544 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	v. Jan 31, 2020	data reduction
XSCALE	v. Jan 31, 2020	data scaling
MOLREP	Vers 11.6.03; 30.04.2018	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NFQ

6nfq

Resolution: 2.15→40.062 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.946 / SU B: 7.524 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2634	787	5.118 %
R_work	0.2147	14591	-
all	0.217	-	-
obs	-	15378	99.955 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 67.356 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.153 Å²	-0 Å²	-0 Å²
2-	-	0.153 Å²	-0 Å²
3-	-	-	-0.305 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→40.062 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1396	0	13	87	1496

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	1467
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	1397
X-RAY DIFFRACTION	r_angle_refined_deg	1.644	1.643	2007
X-RAY DIFFRACTION	r_angle_other_deg	1.278	1.581	3239
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.217	5	197
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.677	24.694	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.742	15	226
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.328	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	208
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1653
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	279
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	336
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	1240
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	651
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	654
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.227	0.2	97
X-RAY DIFFRACTION	r_metal_ion_refined	0.156	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.327	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.294	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.301	0.2	2
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.147	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	6.518	7.056	786
X-RAY DIFFRACTION	r_mcbond_other	6.526	7.042	783
X-RAY DIFFRACTION	r_mcangle_it	8.825	10.532	983
X-RAY DIFFRACTION	r_mcangle_other	8.825	10.532	983
X-RAY DIFFRACTION	r_scbond_it	6.067	7.392	681
X-RAY DIFFRACTION	r_scbond_other	5.985	7.381	678
X-RAY DIFFRACTION	r_scangle_it	8.885	10.905	1024
X-RAY DIFFRACTION	r_scangle_other	8.852	10.881	1019
X-RAY DIFFRACTION	r_lrange_it	12.162	86.768	1579
X-RAY DIFFRACTION	r_lrange_other	12.182	86.698	1565

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.15-2.206	0.366	66	0.394	1069	X-RAY DIFFRACTION	99.6488
2.206-2.266	0.386	56	0.364	1054	X-RAY DIFFRACTION	100
2.266-2.332	0.376	40	0.316	1025	X-RAY DIFFRACTION	100
2.332-2.403	0.306	37	0.285	1024	X-RAY DIFFRACTION	100
2.403-2.482	0.343	66	0.305	940	X-RAY DIFFRACTION	100
2.482-2.569	0.258	42	0.265	918	X-RAY DIFFRACTION	100
2.569-2.666	0.353	44	0.289	904	X-RAY DIFFRACTION	100
2.666-2.774	0.371	38	0.276	871	X-RAY DIFFRACTION	100
2.774-2.897	0.327	47	0.246	825	X-RAY DIFFRACTION	100
2.897-3.039	0.297	51	0.219	764	X-RAY DIFFRACTION	100
3.039-3.202	0.268	40	0.24	769	X-RAY DIFFRACTION	100
3.202-3.396	0.341	50	0.26	701	X-RAY DIFFRACTION	100
3.396-3.63	0.292	31	0.237	679	X-RAY DIFFRACTION	100
3.63-3.919	0.308	31	0.23	612	X-RAY DIFFRACTION	99.8447
3.919-4.292	0.247	37	0.175	584	X-RAY DIFFRACTION	100
4.292-4.795	0.205	34	0.15	521	X-RAY DIFFRACTION	100
4.795-5.531	0.21	26	0.16	454	X-RAY DIFFRACTION	100
5.531-6.759	0.246	19	0.195	399	X-RAY DIFFRACTION	100
6.759-9.498	0.212	21	0.17	301	X-RAY DIFFRACTION	100
9.498-40.06	0.152	11	0.182	177	X-RAY DIFFRACTION	98.9474

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Protein , 1 types, 2 molecules AAABBB

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Non-polymers , 6 types, 93 molecules

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