PDB-7bk5: PfCopC mutant - E27A

ID or keywords:

Entry

Database: PDB / ID: 7bk5

Title

PfCopC mutant - E27A

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: 1.54 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	7bk5.cif.gz	37.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7bk5.ent.gz		Display	PDB format
PDBx/mmJSON format	7bk5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7bk5_validation.pdf.gz	920.3 KB	Display	wwPDB validaton report
Full document	7bk5_full_validation.pdf.gz	920.8 KB	Display
Data in XML	7bk5_validation.xml.gz	7.3 KB	Display
Data in CIF	7bk5_validation.cif.gz	9.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bk/7bk5 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bk5	HTTPS FTP

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Related structure data

Related structure data	7bk6C 7bk7C 6nfqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6nfs-d 7bk6-2 6nfq-3 6nfq-2 7bk6-1 6dg6-6 3tqm-1 3zzp-d 2w2u-2 2ywq-1 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

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	27.000, 76.910, 81.950
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	AAA-332- HOH
2	1	AAA-365- HOH

#1: Protein	Putative copper resistance protein / CopC from Pseudomonas fluorescens Mass: 10052.258 Da / Num. of mol.: 1 / Mutation: E27A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain SBW25) (bacteria) Strain: SBW25 / Gene: PFLU_3946 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C3JYL7
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.87 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.52 M ammonium phosphate dibasic, 0.09 M Tris, 3% (w/v) D-sorbitol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.54→50 Å / Num. obs: 13059 / % possible obs: 99.9 % / Redundancy: 5.47 % / CC_1/2: 0.998 / R_rim(I) all: 0.01011 / Net I/σ(I): 10.11
Reflection shell	Resolution: 1.54→1.58 Å / Num. unique obs: 1822 / CC_1/2: 0.525 / R_rim(I) all: 0.1753

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	VERSION Jan 31, 2020	data reduction
XSCALE	VERSION Jan 31, 2020	data scaling
MOLREP	Vers 11.7.03; 13.07.2020	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NFQ

6nfq

Resolution: 1.54→40.975 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.963 / SU B: 2.781 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2339	647	4.954 %
R_work	0.2055	12412	-
all	0.207	-	-
obs	-	13059	99.939 %

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: 28.664 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.918 Å²	0 Å²	-0 Å²
2-	-	-0.915 Å²	0 Å²
3-	-	-	-1.003 Å²

Refinement step

Cycle: LAST / Resolution: 1.54→40.975 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	708	0	10	92	810

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	780
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	743
X-RAY DIFFRACTION	r_angle_refined_deg	1.748	1.644	1071
X-RAY DIFFRACTION	r_angle_other_deg	1.291	1.587	1731
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.143	5	107
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	46.238	25	26
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.149	15	125
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.732	15	1
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	108
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	893
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	149
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	144
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	580
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	336
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	334
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.269	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.256	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.178	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.181	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.247	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.28	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.785	2.819	416
X-RAY DIFFRACTION	r_mcbond_other	2.772	2.818	415
X-RAY DIFFRACTION	r_mcangle_it	3.981	4.205	527
X-RAY DIFFRACTION	r_mcangle_other	3.982	4.208	528
X-RAY DIFFRACTION	r_scbond_it	3.553	3.138	364
X-RAY DIFFRACTION	r_scbond_other	3.489	3.107	361
X-RAY DIFFRACTION	r_scangle_it	5.368	4.563	544
X-RAY DIFFRACTION	r_scangle_other	5.274	4.517	539
X-RAY DIFFRACTION	r_lrange_it	7.771	36.042	808
X-RAY DIFFRACTION	r_lrange_other	7.564	35.263	779

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.54-1.58	0.415	53	0.417	897	0.417	950	0.556	0.629	100	0.405
1.58-1.623	0.307	38	0.356	867	0.354	905	0.751	0.724	100	0.338
1.623-1.67	0.338	50	0.31	844	0.312	894	0.811	0.817	100	0.291
1.67-1.722	0.3	42	0.285	839	0.286	881	0.858	0.852	100	0.259
1.722-1.778	0.335	43	0.27	821	0.273	864	0.844	0.879	100	0.245
1.778-1.84	0.339	40	0.266	765	0.269	805	0.848	0.876	100	0.24
1.84-1.909	0.306	41	0.268	759	0.27	800	0.861	0.877	100	0.242
1.909-1.987	0.293	31	0.273	734	0.274	765	0.871	0.88	100	0.259
1.987-2.075	0.378	44	0.243	706	0.25	750	0.825	0.893	100	0.235
2.075-2.176	0.339	26	0.249	661	0.252	687	0.864	0.904	100	0.241
2.176-2.294	0.275	32	0.248	657	0.249	690	0.938	0.909	99.8551	0.243
2.294-2.432	0.267	28	0.214	608	0.217	636	0.925	0.919	100	0.219
2.432-2.6	0.349	35	0.221	558	0.227	593	0.886	0.924	100	0.226
2.6-2.807	0.189	22	0.191	543	0.191	565	0.953	0.945	100	0.213
2.807-3.074	0.269	22	0.191	502	0.194	525	0.912	0.948	99.8095	0.219
3.074-3.434	0.219	35	0.174	449	0.177	485	0.947	0.959	99.7938	0.203
3.434-3.961	0.15	23	0.153	402	0.153	425	0.973	0.97	100	0.185
3.961-4.839	0.138	17	0.142	348	0.142	365	0.982	0.978	100	0.192
4.839-6.797	0.184	21	0.162	282	0.164	303	0.974	0.973	100	0.223
6.797-40.975	0.135	4	0.189	170	0.188	179	0.97	0.965	97.2067	0.303

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