PDB-2qev: Crystal Structure of Anopheles gambiae D7r4

ID or keywords:

Entry

Database: PDB / ID: 2qev

Title

Crystal Structure of Anopheles gambiae D7r4

Components

D7R4 Protein

Keywords

LIGAND BINDING PROTEIN / All-helical / Odorant-binding protein

Function / homology

Function and homology information

odorant binding / vasodilation / sensory perception of smell / extracellular space
Similarity search - Function

Biological species

Anopheles gambiae (African malaria mosquito)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.998 Å

Authors

Andersen, J.F. / Mans, B.J. / Calvo, E. / Ribeiro, J.M.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure of D7r4, a Salivary Biogenic Amine-binding Protein from the Malaria Mosquito Anopheles gambiae
Authors: Mans, B.J. / Calvo, E. / Ribeiro, J.M. / Andersen, J.F.

History

Deposition	Jun 26, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Oct 30, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2qev.cif.gz	45.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2qev.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2qev_validation.pdf.gz	423.5 KB	Display	wwPDB validaton report
Full document	2qev_full_validation.pdf.gz	426.6 KB	Display
Data in XML	2qev_validation.xml.gz	9.6 KB	Display
Data in CIF	2qev_validation.cif.gz	12 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qe/2qev ftp://data.pdbj.org/pub/pdb/validation_reports/qe/2qev	HTTPS FTP

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Related structure data

Related structure data	2pqlC 2qebC 2qehC 2qeoC C: citing same article (ref.)
Similar structure data	2pql-d 2qeo-2 2qeb-1 1myt-d 2qeo-1 3qm5-d 2qeh-d 3qm6-d 2qeb-2 2nrl-d 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

A: D7R4 Protein

17.1 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)	62.651, 62.651, 42.773
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	D7R4 Protein / D7-related 4 protein Mass: 17099.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Strain: G3 / Gene: D7r4 / Plasmid: pET17B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9BIH3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.45 Å³/Da / Density % sol: 49.87 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20 % PEG 6000, 0.1 M Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9791533 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2005 / Details: mirrors

Radiation

Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9791533 Å / Relative weight: 1

Reflection

D res high: 2.5 Å / D res low: 30 Å / % possible obs: 99.9

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs
3	1	7.8	34578	0.039	0.45	11430
4.9	2	6.6	56172	0.071	0.76	11400

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.38	30	99.3	1	0.026	0.544	2.9
4.27	5.38	100	1	0.028	0.481	3
3.73	4.27	99.9	1	0.03	0.44	3.1
3.39	3.73	100	1	0.036	0.432	3.1
3.15	3.39	100	1	0.05	0.565	3.1
2.96	3.15	100	1	0.067	0.363	3.1
2.82	2.96	100	1	0.109	0.365	3.1
2.69	2.82	100	1	0.166	0.575	3.1
2.59	2.69	100	1	0.192	0.356	3
2.5	2.59	99.8	1	0.259	0.386	2.9
5.38	30	99.5	2	0.039	1.016	4.8
4.27	5.38	100	2	0.049	1.151	5
3.73	4.27	100	2	0.059	1.107	5
3.39	3.73	100	2	0.077	1.003	5.1
3.15	3.39	100	2	0.103	0.755	5.1
2.96	3.15	100	2	0.136	0.594	5.1
2.82	2.96	100	2	0.228	0.488	5.1
2.69	2.82	100	2	0.338	0.547	5
2.59	2.69	100	2	0.396	0.431	4.9
2.5	2.59	99.2	2	0.546	0.519	4.3

Reflection

Resolution: 1.998→62.62 Å / Num. all: 11190 / Num. obs: 11190 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / R_merge(I) obs: 0.039 / Χ²: 1.341 / Net I/σ(I): 18.3

Reflection shell

Resolution: 1.998→2.07 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.303 / Mean I/σ(I) obs: 3.3 / Num. unique all: 941 / Χ²: 0.905 / % possible all: 84.3

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.49 Å / D res low: 50 Å / FOM : 0.4 / FOM acentric: 0.408 / FOM centric: 0.31 / Reflection: 5940 / Reflection acentric: 5448 / Reflection centric: 492

Phasing MAD set

Highest resolution: 2.49 Å / Lowest resolution: 50 Å / Reflection centric: 492

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric
1	1.67	1	0	0	0	0	5448
2	0.81	0.74	3.4	4.8	1.02	0.89	5445

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	14.77-50	1.01	1	0.2	0.1	0	0	16	10
1	8.67-14.77	0.98	1	0.2	0.1	0	0	95	28
1	6.13-8.67	1.96	1	0.2	0.1	0	0	226	41
1	4.74-6.13	1.49	1	0.1	0.1	0	0	414	55
1	3.87-4.74	1.22	1	0.1	0	0	0	675	69
1	3.27-3.87	1.46	1	0	0	0	0	962	81
1	2.83-3.27	7.12	1	0	0	0	0	1336	99
1	2.49-2.83	2.69	1	0	0	0	0	1724	109
2	14.77-50	0.52	0.7	6.8	9.7	1.99	1.9	16	10
2	8.67-14.77	0.61	0.54	6	8.5	2.4	1.72	95	28
2	6.13-8.67	0.53	0.47	4.4	4.5	2.52	2.18	226	41
2	4.74-6.13	0.61	0.63	4.5	6.2	1.85	1.07	414	55
2	3.87-4.74	0.78	0.79	4.7	5.8	1.14	0.71	675	69
2	3.27-3.87	0.86	0.91	4	4.9	0.85	0.53	962	81
2	2.83-3.27	0.93	0.98	3	3.6	0.65	0.39	1335	99
2	2.49-2.83	0.99	1.01	2.3	3	0.46	0.3	1722	109

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	65.35519	0.735	0.596	0.048	0
2	Se	61.07232	0.885	0.677	0.274	0
3	Se	141.81461	0.763	0.562	0.338	0
4	Se	83.957	0.883	0.816	0.094	0
5	Se	59.45215	0.735	0.597	0.057	0.157
6	Se	72.06138	0.886	0.677	0.277	0.149
7	Se	117.02042	0.763	0.563	0.341	0.164
8	Se	84.49219	0.883	0.819	0.093	0.12

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
14.77-50	0.781	0.808	0.737	26	16	10
8.67-14.77	0.805	0.828	0.723	123	95	28
6.13-8.67	0.818	0.851	0.634	267	226	41
4.74-6.13	0.773	0.797	0.599	469	414	55
3.87-4.74	0.634	0.658	0.396	744	675	69
3.27-3.87	0.492	0.512	0.263	1043	962	81
2.83-3.27	0.31	0.324	0.125	1435	1336	99
2.49-2.83	0.134	0.14	0.047	1833	1724	109

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 5940

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.77-100	47.7	0.887	501
4.56-5.77	38.9	0.927	506
3.96-4.56	47.2	0.903	505
3.59-3.96	46.2	0.902	504
3.33-3.59	50.3	0.888	502
3.13-3.33	54.3	0.864	502
2.98-3.13	53.4	0.886	503
2.84-2.98	60.2	0.869	515
2.73-2.84	68.7	0.856	502
2.64-2.73	72.5	0.827	512
2.49-2.64	76.8	0.799	888

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
EPICS-based	data aquisition system	data collection
HKL-3000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.998→62.62 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.948 / SU B: 11.1 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.213 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	533	4.8 %	RANDOM
R_work	0.219	-	-	-
obs	0.22	11190	98.15 %	-
all	-	11190	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.093 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.53 Å²	0 Å²	0 Å²
2-	-	0.53 Å²	0 Å²
3-	-	-	-1.07 Å²

Refinement step

Cycle: LAST / Resolution: 1.998→62.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1189	0	0	72	1261

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1215
X-RAY DIFFRACTION	r_angle_refined_deg	1.06	1.977	1634
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.822	5	144
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.372	24	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.942	15	237
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.589	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	175
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	908
X-RAY DIFFRACTION	r_nbd_refined	0.259	0.3	591
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.5	849
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.5	104
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.225	0.3	23
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.5	7
X-RAY DIFFRACTION	r_mcbond_it	3.919	1.5	740
X-RAY DIFFRACTION	r_mcangle_it	5.006	2	1175
X-RAY DIFFRACTION	r_scbond_it	7.095	3	518
X-RAY DIFFRACTION	r_scangle_it	9.833	4.5	459

LS refinement shell

Resolution: 1.998→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	31	-
R_work	0.317	695	-
obs	-	726	85.82 %

Refinement TLS params.

Method: refined / Origin x: 8.3779 Å / Origin y: -22.4167 Å / Origin z: 0.7442 Å

	11	12	13	21	22	23	31	32	33
T	-0.0441 Å²	0.0299 Å²	-0.0256 Å²	-	0.0604 Å²	-0.072 Å²	-	-	-0.033 Å²
L	1.853 °²	0.0847 °²	1.1752 °²	-	0.5588 °²	0.3301 °²	-	-	1.714 °²
S	-0.2977 Å °	-0.0943 Å °	0.2868 Å °	-0.0688 Å °	0.1145 Å °	-0.0708 Å °	-0.2412 Å °	-0.2394 Å °	0.1832 Å °

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