PDB-5n7x: CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE EWVHPQFEQKAK

ID or keywords:

Entry

Database: PDB / ID: 5n7x

Title

CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE EWVHPQFEQKAK

Components

GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide
Streptavidin

Keywords

BIOTIN BINDING PROTEIN / STREPTAVIDIN / HPQ MOTIF / STREPTAVIDIN PEPTIDE 11101 COMPLEX

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

Streptomyces avidinii (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.12 Å

Authors

Lyamichev, V. / Goodrich, L. / Sullivan, E. / Bannen, R. / Benz, J. / Albert, T. / Patel, J.

Citation

Journal: Sci Rep / Year: 2017
Title: Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target.
Authors: Lyamichev, V.I. / Goodrich, L.E. / Sullivan, E.H. / Bannen, R.M. / Benz, J. / Albert, T.J. / Patel, J.J.

History

Deposition	Feb 21, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5n7x.cif.gz	480.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5n7x.ent.gz	397.3 KB	Display	PDB format
PDBx/mmJSON format	5n7x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5n7x_validation.pdf.gz	502.3 KB	Display	wwPDB validaton report
Full document	5n7x_full_validation.pdf.gz	511.7 KB	Display
Data in XML	5n7x_validation.xml.gz	53.4 KB	Display
Data in CIF	5n7x_validation.cif.gz	79.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n7/5n7x ftp://data.pdbj.org/pub/pdb/validation_reports/n7/5n7x	HTTPS FTP

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Related structure data

Related structure data	5n89C 5n8bC 5n8eC 5n8jC 5n8tC 5n8wC 5n99C C: citing same article (ref.)
Similar structure data	3rdx-d 2zsc-d 3dkz-d 6ivc-1 3mwn-d 6ork-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Streptavidin

B: Streptavidin

C: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

D: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

E: Streptavidin

F: Streptavidin

G: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

H: Streptavidin

I: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

J: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

K: Streptavidin

L: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

M: Streptavidin

N: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

O: Streptavidin

P: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

163 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Streptavidin

D: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

K: Streptavidin

L: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

defined by software
40.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Streptavidin

C: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

M: Streptavidin

N: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

defined by software
40.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Streptavidin

I: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

O: Streptavidin

P: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

defined by software
40.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

F: Streptavidin

G: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

H: Streptavidin

J: GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide

defined by software
40.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.913, 64.806, 81.156
Angle α, β, γ (deg.)	96.31, 97.15, 84.09
Int Tables number	1
Space group name H-M	P1

#1: Protein	Streptavidin Mass: 18849.672 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide	GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide Mass: 1529.714 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1270 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.83 Å³/Da / Density % sol: 32.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Magnesium acetate 0.1M Sodium cacodylate pH 6.5 15% PEG6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 1.12→80.13 Å / Num. obs: 403025 / % possible obs: 90.4 % / Redundancy: 1.66 % / CC_1/2: 0.99 / R_merge(I) obs: 0.031 / Net I/σ(I): 10.03
Reflection shell	Resolution: 1.12→1.22 Å / Redundancy: 1.58 % / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 86936 / CC_1/2: 0.37 / % possible all: 86.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
SADABS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.12→80.13 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.97 / SU B: 1.63 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18554	20178	5 %	RANDOM
R_work	0.16023	-	-	-
obs	0.16149	382815	90.36 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 18.773 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	-1 Å²	-0.24 Å²
2-	-	-0.16 Å²	0.95 Å²
3-	-	-	0.08 Å²

Refinement step

Cycle: 1 / Resolution: 1.12→80.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8074	0	0	1270	9344

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.02	8640
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	7367
X-RAY DIFFRACTION	r_angle_refined_deg	1.58	1.89	11914
X-RAY DIFFRACTION	r_angle_other_deg	0.937	3	17118
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.671	5	1162
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.554	24.072	388
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.586	15	1207
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.987	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	1308
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	10031
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1952
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.743	1.288	4352
X-RAY DIFFRACTION	r_mcbond_other	1.742	1.287	4351
X-RAY DIFFRACTION	r_mcangle_it	2.204	1.925	5442
X-RAY DIFFRACTION	r_mcangle_other	2.204	1.926	5443
X-RAY DIFFRACTION	r_scbond_it	2.171	1.507	4288
X-RAY DIFFRACTION	r_scbond_other	2.171	1.508	4289
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.576	2.163	6413
X-RAY DIFFRACTION	r_long_range_B_refined	3.405	25.685	37294
X-RAY DIFFRACTION	r_long_range_B_other	2.783	24.197	35839
X-RAY DIFFRACTION	r_rigid_bond_restr	2.438	3	16007
X-RAY DIFFRACTION	r_sphericity_free	32.327	5	182
X-RAY DIFFRACTION	r_sphericity_bonded	11.585	5	16813

LS refinement shell

Resolution: 1.12→1.149 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.365	1396	-
R_work	0.341	26734	-
obs	-	-	85.35 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.2239	-0.0809	-0.0817	0.099	0.0194	0.1946	-0.0254	-0.0047	-0.0294	0.0129	0.0071	0.0059	-0.0075	-0.0326	0.0183	0.0424	0.0262	0.0003	0.0294	-0.0168	0.0274	-87.1658	-112.8953	-16.8744
2	0.1442	-0.0502	-0.0422	0.1956	0.0072	0.095	-0.0125	-0.0584	0.0024	0.0147	0.0078	-0.0064	0.0194	0.026	0.0047	0.0447	0.0281	0.0009	0.0498	-0.0184	0.0289	-102.9053	-95.2951	23.9778
3	0.2872	-0.2528	-0.3811	0.4766	0.4483	0.5578	-0.013	-0.0851	0.0557	0.0514	0.0918	-0.0824	0.0353	0.1114	-0.0789	0.0342	0.0281	-0.0089	0.0704	-0.0497	0.0487	-89.6246	-87.6275	20.7389
4	0.7342	-0.4957	0.1364	0.3357	-0.1366	2.3899	-0.0269	-0.0013	-0.0924	0.0197	0.0096	0.0602	0.0085	-0.3013	0.0173	0.0236	0.0151	0.0036	0.0685	-0.0302	0.0505	-98.8298	-119.0864	-24.8822
5	0.1938	-0.0459	-0.0844	0.1385	0.0229	0.1709	-0.0348	-0.0222	-0.0423	0.0286	0.02	-0.0004	0.026	0.019	0.0147	0.0481	0.0299	0.0011	0.0251	-0.012	0.0358	-73.4044	-122.5023	-15.0749
6	0.2132	-0.0838	-0.1037	0.1466	0.0235	0.139	-0.0107	-0.0599	0.02	0.0111	0.0135	0.0061	0.0097	0.0086	-0.0028	0.0402	0.0228	-0.0001	0.0459	-0.026	0.0312	-116.9609	-86.0217	23.9035
7	0.1479	-0.1819	0.2867	0.2891	-0.1117	1.4515	-0.0078	-0.0238	-0.0312	0.0157	0.003	0.0563	0.0289	-0.1315	0.0048	0.0328	0.0156	0.0027	0.0409	-0.0244	0.039	-129.1112	-92.036	16.4757
8	0.2317	-0.0848	-0.0873	0.1103	0.0299	0.2003	0.0117	0.011	0.015	-0.0198	-0.0134	-0.0024	0.0219	-0.0006	0.0017	0.0426	0.0262	-0.0008	0.0266	-0.0161	0.0259	-104.4843	-94.6178	-4.061
9	0.082	-0.3313	-0.0108	1.5237	-0.1942	0.3084	-0.024	-0.0152	0.0332	0.0641	0.016	-0.1488	0.0376	0.0596	0.008	0.037	0.0302	-0.0098	0.0373	-0.0219	0.0442	-59.9523	-115.6071	-18.0405
10	0.2067	-0.0871	0.3054	0.842	0.147	0.7941	0.0301	0.0271	-0.0471	0.0185	-0.0106	0.0293	0.1002	-0.0201	-0.0195	0.0627	0.016	-0.0021	0.0311	-0.0253	0.0346	-113.9395	-106.155	-0.8776
11	0.2726	-0.0788	-0.1408	0.1126	0.0766	0.2165	-0.0174	0.0517	-0.0432	-0.0025	-0.0094	0.0019	0.0184	-0.0224	0.0268	0.0327	0.0181	0.0011	0.0401	-0.0308	0.0362	-72.6449	-124.0174	-43.0595
12	0.0303	0.0363	0.2182	0.5505	-0.1142	2.4327	0.007	0.008	-0.0243	-0.0287	-0.0174	-0.0141	0.1977	-0.1289	0.0104	0.0612	-0.0128	0.0243	0.0809	-0.0764	0.0883	-83.0968	-135.0455	-39.8641
13	0.1767	-0.0626	-0.0998	0.0971	0.0622	0.1382	0.0303	0.0105	0.0506	-0.0265	-0.0153	-0.0084	-0.0307	-0.0209	-0.0149	0.0437	0.0279	0.004	0.0248	-0.0128	0.0406	-110.6097	-79.0894	-2.3829
14	0.5249	-0.2566	0.381	0.2061	-0.0545	1.2073	0.0324	-0.0077	0.1647	-0.0221	0.0094	-0.0688	-0.1208	0.0286	-0.0418	0.0565	0.0174	0.026	0.0196	-0.0215	0.1089	-101.7653	-68.9119	5.4093
15	0.1696	-0.0575	-0.1014	0.1048	0.0867	0.1485	0.0181	0.0604	0.0027	-0.0229	-0.018	-0.0035	-0.0318	-0.0427	-0.0001	0.0386	0.0285	-0.0016	0.0466	-0.0164	0.0254	-78.4967	-108.1172	-42.9784
16	0.3905	-0.2693	-0.2197	0.2016	0.2693	1.0495	0.0457	-0.0009	0.0732	-0.0363	0.0089	-0.0541	-0.1215	0.0074	-0.0546	0.056	0.0259	0.0113	0.026	-0.0141	0.0395	-69.9435	-97.7142	-35.3612

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 135
2	X-RAY DIFFRACTION	2	B	14 - 134
3	X-RAY DIFFRACTION	3	C	1 - 11
4	X-RAY DIFFRACTION	4	D	1 - 11
5	X-RAY DIFFRACTION	5	E	14 - 135
6	X-RAY DIFFRACTION	6	F	14 - 135
7	X-RAY DIFFRACTION	7	G	1 - 11
8	X-RAY DIFFRACTION	8	H	14 - 135
9	X-RAY DIFFRACTION	9	I	1 - 11
10	X-RAY DIFFRACTION	10	J	1 - 11
11	X-RAY DIFFRACTION	11	K	14 - 135
12	X-RAY DIFFRACTION	12	L	1 - 11
13	X-RAY DIFFRACTION	13	M	14 - 134
14	X-RAY DIFFRACTION	14	N	1 - 11
15	X-RAY DIFFRACTION	15	O	14 - 135
16	X-RAY DIFFRACTION	16	P	1 - 11

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