PDB-7w8f: Crystal structure of siderophore binding protein VatD from Vibrio...

ID or keywords:

Entry

Database: PDB / ID: 7w8f

Title

Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal

Components

Putative periplasm binding protein

Keywords

METAL BINDING PROTEIN / periplasmic iron-compound binding protein / Deferoxamine complex

Function / homology

Function and homology information

aerobactin transport / ferric-hydroxamate import into cell / siderophore transmembrane transport / ATP-binding cassette (ABC) transporter complex / iron ion transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / periplasmic space
Similarity search - Function

Biological species

Vibrio vulnificus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Tomoo, K. / Miyamoto, K.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of siderophore binding protein VatD from Vibrio vulnificus M2799 complexed with Desferal
Authors: Tomoo, K. / Miyamoto, K.

History

Deposition	Dec 7, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 7, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7w8f.cif.gz	79.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7w8f.ent.gz	53 KB	Display	PDB format
PDBx/mmJSON format	7w8f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7w8f_validation.pdf.gz	835.2 KB	Display	wwPDB validaton report
Full document	7w8f_full_validation.pdf.gz	839.1 KB	Display
Data in XML	7w8f_validation.xml.gz	14.7 KB	Display
Data in CIF	7w8f_validation.cif.gz	20.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w8/7w8f ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w8f	HTTPS FTP

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Related structure data

Related structure data	1efdS S: Starting model for refinement
Similar structure data	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

A: Putative periplasm binding protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	34.800, 57.890, 62.700
Angle α, β, γ (deg.)	90.000, 95.020, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative periplasm binding protein Mass: 31094.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: fhuD / Production host: Escherichia coli (E. coli) / References: UniProt: Q845T3
#2: Chemical	ChemComp-KTY / desferrioxamine B / N~4~-{5-[acetyl(hydroxy)amino]pentyl}-N~1~-[5-({4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoyl}amino)pentyl]-N~1~-hydr oxybutanediamide Mass: 560.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₄₈N₆O₈ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.02 Å³/Da / Density % sol: 39.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30%(w/v) PEG-3,350, 50mM MgCl2, 0.1M Bis-Tris pH6.5

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Data collection

Diffraction	Mean temperature: 130 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 15, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.85→26.3 Å / Num. obs: 20814 / % possible obs: 97.6 % / Redundancy: 3.48 % / R_merge(I) obs: 0.085 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.85→1.92 Å / R_merge(I) obs: 0.345 / Num. unique obs: 2172

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
CrystalClear		data reduction
CrystalClear		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1EFD

1efd

Resolution: 1.9→26.103 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.943 / WR_factor R_free: 0.199 / WR_factor R_work: 0.163 / SU B: 4.007 / SU ML: 0.115 / Average fsc free: 0.9181 / Average fsc work: 0.9315 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2187	982	5.101 %
R_work	0.1765	18269	-
all	0.179	-	-
obs	-	19251	97.775 %

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: 25.187 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.017 Å²	-0 Å²	-0.009 Å²
2-	-	0.004 Å²	0 Å²
3-	-	-	0.014 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→26.103 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2174	0	41	161	2376

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2253
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2165
X-RAY DIFFRACTION	r_angle_refined_deg	1.628	1.66	3054
X-RAY DIFFRACTION	r_angle_other_deg	1.377	1.605	5002
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.212	5	277
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.234	23.727	110
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.324	15	389
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.54	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	307
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2516
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	484
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	466
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	2077
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	1100
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1084
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	135
X-RAY DIFFRACTION	r_metal_ion_refined	0.043	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.279	0.2	9
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.146	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.861	2.363	1111
X-RAY DIFFRACTION	r_mcbond_other	1.845	2.36	1110
X-RAY DIFFRACTION	r_mcangle_it	2.67	3.538	1387
X-RAY DIFFRACTION	r_mcangle_other	2.67	3.54	1388
X-RAY DIFFRACTION	r_scbond_it	3.039	2.855	1142
X-RAY DIFFRACTION	r_scbond_other	3.037	2.855	1143
X-RAY DIFFRACTION	r_scangle_it	4.868	4.109	1667
X-RAY DIFFRACTION	r_scangle_other	4.866	4.109	1668
X-RAY DIFFRACTION	r_lrange_it	6.099	29.336	2522
X-RAY DIFFRACTION	r_lrange_other	6.085	29.225	2505

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
1.9-1.949	0.432	64	0.272	1336	0.279	1454	0.793	0.852	96.2861	0.266
1.949-2.002	0.233	67	0.243	1261	0.242	1379	0.902	0.888	96.3017	0.238
2.002-2.06	0.243	62	0.21	1285	0.212	1384	0.905	0.91	97.3266	0.205
2.06-2.123	0.265	64	0.204	1212	0.207	1310	0.903	0.922	97.4046	0.198
2.123-2.192	0.235	62	0.191	1202	0.193	1304	0.926	0.93	96.9325	0.18
2.192-2.268	0.275	66	0.186	1114	0.191	1222	0.901	0.932	96.563	0.175
2.268-2.353	0.241	63	0.194	1111	0.197	1210	0.917	0.92	97.0248	0.186
2.353-2.449	0.254	48	0.177	1077	0.181	1158	0.927	0.937	97.1503	0.171
2.449-2.556	0.281	59	0.178	1026	0.183	1111	0.889	0.934	97.6598	0.166
2.556-2.68	0.229	50	0.164	1014	0.167	1078	0.934	0.952	98.7013	0.156
2.68-2.823	0.21	35	0.162	963	0.163	1006	0.946	0.953	99.2048	0.147
2.823-2.992	0.266	54	0.178	913	0.182	971	0.924	0.946	99.5881	0.161
2.992-3.196	0.265	43	0.177	847	0.181	892	0.912	0.944	99.7758	0.161
3.196-3.448	0.2	40	0.16	818	0.162	862	0.952	0.963	99.536	0.149
3.448-3.77	0.178	49	0.165	724	0.166	773	0.962	0.967	100	0.155
3.77-4.204	0.147	45	0.159	660	0.158	709	0.97	0.966	99.4358	0.15
4.204-4.834	0.199	38	0.142	590	0.147	628	0.968	0.969	100	0.135
4.834-5.87	0.179	33	0.168	503	0.168	539	0.962	0.972	99.4434	0.16
5.87-8.099	0.205	22	0.19	404	0.191	428	0.972	0.967	99.5327	0.175
8.099-26.103	0.181	18	0.16	208	0.161	259	0.968	0.978	87.2587	0.151

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