PDB-5n99: CRYSTAL STRUCTURE OF STREPTAVIDIN with cyclic peptide NQpWQ

ID or keywords:

Entry

Database: PDB / ID: 5n99

Title

CRYSTAL STRUCTURE OF STREPTAVIDIN with cyclic peptide NQpWQ

Components

ASN-GLN-DPR-TRP-GLN
Streptavidin

Keywords

Biotin binding protein / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACID / STREPTAVIDIN CYCLIC PEPTIDE COMPLEX

Function / homology

Function and homology information

biotin binding / extracellular region
Similarity search - Function

Biological species

Streptomyces avidinii (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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 24, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5n99.cif.gz	630 KB	Display	PDBx/mmCIF format
PDB format	pdb5n99.ent.gz	537.2 KB	Display	PDB format
PDBx/mmJSON format	5n99.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5n99_validation.pdf.gz	546.4 KB	Display	wwPDB validaton report
Full document	5n99_full_validation.pdf.gz	559.3 KB	Display
Data in XML	5n99_validation.xml.gz	78.5 KB	Display
Data in CIF	5n99_validation.cif.gz	115.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n9/5n99 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/5n99	HTTPS FTP

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Related structure data

Related structure data	5n7xC 5n89C 5n8bC 5n8eC 5n8jC 5n8tC 5n8wC C: citing same article (ref.)
Similar structure data	4bx5-d 4cpi-2 2rtb-1 2izd-1 2rta-1 6s50-d 6t31-1 2on7-2 4dne-1 6lng-1 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: ASN-GLN-DPR-TRP-GLN

D: Streptavidin

E: ASN-GLN-DPR-TRP-GLN

F: ASN-GLN-DPR-TRP-GLN

G: Streptavidin

H: ASN-GLN-DPR-TRP-GLN

I: Streptavidin

J: ASN-GLN-DPR-TRP-GLN

K: Streptavidin

L: ASN-GLN-DPR-TRP-GLN

M: Streptavidin

N: ASN-GLN-DPR-TRP-GLN

O: Streptavidin

P: ASN-GLN-DPR-TRP-GLN

Q: Streptavidin

R: ASN-GLN-DPR-TRP-GLN

S: Streptavidin

T: ASN-GLN-DPR-TRP-GLN

U: Streptavidin

V: ASN-GLN-DPR-TRP-GLN

X: ASN-GLN-DPR-TRP-GLN

Y: Streptavidin

234 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Streptavidin

B: Streptavidin

C: ASN-GLN-DPR-TRP-GLN

D: Streptavidin

E: ASN-GLN-DPR-TRP-GLN

F: ASN-GLN-DPR-TRP-GLN

M: Streptavidin

N: ASN-GLN-DPR-TRP-GLN

defined by author&software
78.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Streptavidin

H: ASN-GLN-DPR-TRP-GLN

I: Streptavidin

J: ASN-GLN-DPR-TRP-GLN

K: Streptavidin

L: ASN-GLN-DPR-TRP-GLN

Q: Streptavidin

R: ASN-GLN-DPR-TRP-GLN

defined by author&software
78.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

O: Streptavidin

P: ASN-GLN-DPR-TRP-GLN

S: Streptavidin

T: ASN-GLN-DPR-TRP-GLN

U: Streptavidin

V: ASN-GLN-DPR-TRP-GLN

X: ASN-GLN-DPR-TRP-GLN

Y: Streptavidin

defined by author&software
78.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.744, 115.315, 210.369
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Streptavidin Mass: 18849.672 Da / Num. of mol.: 12 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	ASN-GLN-DPR-TRP-GLN Mass: 671.700 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2080 / 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 grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Sodium citrate pH 5.5 15% PEG6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 1.5→48.72 Å / Num. obs: 261661 / % possible obs: 99.7 % / Redundancy: 6.58 % / B_iso Wilson estimate: 19.25 Å² / CC_1/2: 0.999 / R_sym value: 0.079 / Net I/σ(I): 13.3
Reflection shell	Resolution: 1.5→1.6 Å / Redundancy: 5.77 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 44516 / CC_1/2: 0.447 / R_sym value: 0.67 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
BUSTER	2.11.6	refinement
XDS		data reduction
SADABS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→48.72 Å / Cor.coef. F_o:F_c: 0.9634 / Cor.coef. F_o:F_c free: 0.9568 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU R_free Blow DPI: 0.07 / SU R_free Cruickshank DPI: 0.067

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1917	12914	4.94 %	RANDOM
R_work	0.1671	-	-	-
obs	0.1684	261498	99.46 %	-

Displacement parameters

B_iso mean: 23.76 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1908 Å²	0 Å²	0 Å²
2-	-	-0.9359 Å²	0 Å²
3-	-	-	3.1266 Å²

Refine analyze

Luzzati coordinate error obs: 0.177 Å

Refinement step

Cycle: 1 / Resolution: 1.5→48.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11813	0	0	2098	13911

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	12322	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.1	17080	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		3957	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		270	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1957	HARMONIC	5
X-RAY DIFFRACTION	t_it		12322	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	4.49
X-RAY DIFFRACTION	t_other_torsion	13.87
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1727	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		15908	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.5→1.54 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	877	4.88 %
R_work	0.2549	17105	-
all	0.256	17982	-
obs	-	-	93.23 %

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	0.5987	-0.162	0.085	0.4585	-0.0595	0.8619	-0.0267	0.0243	0.068	0.0488	-0.0271	-0.0052	-0.1902	0.021	0.0538	0.0017	-0.0052	-0.0242	-0.0334	0.0086	-0.0098	73.6002	56.4311	26.7617
2	0.937	0.0738	-0.1849	1.0227	-0.1079	1.5951	-0.0344	-0.0178	-0.1897	-0.0752	0.0016	-0.1085	0.4383	-0.0157	0.0328	0.0491	-0.0162	0.0304	-0.0738	0.0158	-0.0326	33.7245	-25.282	13.3147
3	0.6995	-0.0402	0.027	0.6017	0.1315	0.9051	0.0043	0.028	-0.0835	-0.062	0.0224	-0.0802	0.1577	0.1127	-0.0267	-0.0064	0.0156	0.02	-0.0186	-0.0063	-0.0115	76.5245	27.4023	14.9518
4	1.0761	-0.1536	0.0423	0.7215	0.0139	1.161	-0.0035	-0.0008	0.2202	0.0473	0.0269	0.0408	-0.1783	-0.1775	-0.0233	-0.0475	0.0345	0.0078	-0.0211	-0.012	0.0069	45.0529	40.821	45.6082
5	0.4484	-0.0525	0.0854	0.5935	-0.1406	0.8218	-0.0267	0.0205	0.0266	-0.1284	0.0327	0.0714	0.0534	-0.0528	-0.006	-0.0111	-0.013	-0.0033	-0.0075	-0.0037	-0.0249	63.061	37.1163	9.706
6	0.5259	0.0406	-0.0654	0.7717	-0.0059	0.6948	0.0426	-0.0522	0.0409	0.0708	-0.0647	0.0082	-0.0664	-0.0169	0.0221	-0.0044	-0.0025	-0.0125	-0.0082	0.0176	-0.0308	39.6133	3.1272	25.2392
7	0.5184	0.0386	0.0971	0.9124	-0.2058	0.9594	0.0287	0.0134	-0.0742	-0.0018	-0.0111	-0.0363	0.1721	0.0987	-0.0176	-0.0174	0.0118	-0.0053	-0.0201	-0.0039	-0.0157	67.37	21.0749	55.3555
8	0.5374	-0.0745	0.3865	1.0177	-0.2273	1.3192	0.036	0.0254	-0.0436	-0.0246	-0.0666	-0.2069	0.1014	0.2058	0.0306	-0.0387	0.0171	0.0048	-0.0009	0.0425	-0.0034	52.7164	-5.9259	19.413
9	0.323	-0.0553	0.1141	0.6389	0.0662	0.7925	0.0012	-0.0473	0.0648	0.0632	-0.0142	-0.023	-0.0767	0.0511	0.0131	-0.0149	-0.011	-0.0098	-0.0126	-0.0024	-0.0158	67.2141	36.796	61.5454
10	0.7134	0.1203	0.2431	0.6194	-0.0562	1.2372	0.0357	-0.0827	-0.0217	0.0476	0.0226	0.0928	0.1351	-0.2824	-0.0583	-0.0526	-0.0181	0.0049	0.0262	-0.0046	-0.0143	40.4054	25.1697	50.5218
11	0.633	0.0304	-0.3238	0.7799	-0.305	1.0961	-0.0414	0.0608	0.0219	-0.0753	0.0872	0.0817	0.1591	-0.2427	-0.0458	-0.0188	-0.0383	0.0095	0.0203	0.0142	-0.0489	24.1573	-12.3091	8.0838
12	0.7024	-0.1294	0.1919	0.7627	-0.1937	1.2829	-0.0243	0.0868	0.0466	-0.0422	-0.0563	-0.1959	-0.0916	0.334	0.0807	-0.0565	-0.0299	-0.0003	0.0233	0.0412	0.0093	88.7309	51.6167	20.3444
13	0.1237	0.1811	0.0707	0.1709	0.0691	0.0002	0.0011	-0.01	0.0067	0.0081	0.0093	0.0056	0.002	0.0201	-0.0104	-0.0021	-0.0057	0	0.0054	-0.0073	-0.0001	0	0	0
14	0.7896	0.3833	0.1061	0.1946	0.0565	0.0061	-0.0024	-0.0027	-0.0083	-0.0089	-0.0006	0.0109	0.0172	-0.0224	0.003	0.0045	0.0085	0.0122	-0.0042	0.0039	-0.0018	0	0	0
15	0.5395	0.3475	0.0893	0.2241	0.0508	0.0279	-0.0016	-0.0059	-0.0096	-0.0067	0	0.0182	-0.0058	-0.0146	0.0016	0.0089	0.0156	0.0003	0.0019	-0.0006	-0.007	0	0	0
16	0.3061	0.1308	0.3365	0.0438	0.1462	0.2971	0.0002	-0.0044	0	-0.011	0.0047	0.0027	-0.005	0.003	-0.0049	0.0043	-0.0013	0.0069	0.0009	-0.0044	-0.0002	0	0	0
17	0.1096	0.112	0.0913	0.0992	0.0928	0.0825	-0.0002	-0.0001	0.0071	0.0022	0.0128	0.0175	0.0018	-0.0057	-0.0126	-0.0022	0.0013	0.0023	-0.0014	-0.0065	-0.001	0	0	0
18	0.6214	0.3262	0.5925	0.1339	0.275	0.4584	0.0012	0.0014	0.0019	-0.0142	0.0031	0.0219	0.0019	-0.003	-0.0043	-0.0014	0.0019	0.017	-0.0005	0.0033	0.0066	0	0	0
19	0.0913	0.0888	0.1957	0.0812	0.1099	0.0656	0.0071	0.0105	0.0001	-0.0426	-0.0135	-0.0004	0.0101	0.0016	0.0064	-0.0086	-0.0059	0.01	-0.0019	0.0042	0	0	0	0
20	0.7905	-0.2841	0.2157	0.0435	-0.0761	0	-0.0019	0.0062	-0.0018	0.0273	-0.0244	0.0305	0.0313	-0.0426	0.0263	0.0228	-0.0102	0.0124	-0.0152	0.0143	-0.0105	0	0	0
21	0.0235	0.0735	0.1085	0.0901	0.1026	0.1743	-0.0022	-0.0017	0.0032	-0.004	0.0089	0.0022	0.0206	-0.003	-0.0067	-0.004	0.0126	0.0018	0.0013	-0.0041	0.0003	0	0	0
22	0.5582	0.1434	0.2278	0.0388	0.1205	0.0076	-0.0009	-0.0035	-0.0052	0.011	0.0041	0.0446	-0.0056	-0.0025	-0.0031	0.0038	-0.0041	0.0116	0.0015	-0.0058	-0.0134	0	0	0
23	0.1252	-0.1163	0.4365	0.0644	-0.135	0.1703	-0.001	0.0011	0.001	-0.0632	0.0011	0.018	0.0215	-0.0022	-0.0002	-0.0001	0.0131	0.0276	0.0001	-0.0004	-0.0059	0	0	0
24	0.1809	-0.0566	0.1848	0.0083	-0.0384	0.0098	-0.0021	0.0029	0.0066	-0.0173	-0.0006	0.05	-0.0092	-0.0092	0.0027	0.0385	-0.0193	0.0062	0.0013	0.0061	-0.0302	0	0	0

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|* }
2	X-RAY DIFFRACTION	2	{ O\|* }
3	X-RAY DIFFRACTION	3	{ B\|* }
4	X-RAY DIFFRACTION	4	{ Q\|* }
5	X-RAY DIFFRACTION	5	{ D\|* }
6	X-RAY DIFFRACTION	6	{ S\|* }
7	X-RAY DIFFRACTION	7	{ G\|* }
8	X-RAY DIFFRACTION	8	{ U\|* }
9	X-RAY DIFFRACTION	9	{ I\|* }
10	X-RAY DIFFRACTION	10	{ K\|* }
11	X-RAY DIFFRACTION	11	{ Y\|* }
12	X-RAY DIFFRACTION	12	{ M\|* }
13	X-RAY DIFFRACTION	13	{ C\|* }
14	X-RAY DIFFRACTION	14	{ E\|* }
15	X-RAY DIFFRACTION	15	{ F\|* }
16	X-RAY DIFFRACTION	16	{ H\|* }
17	X-RAY DIFFRACTION	17	{ J\|* }
18	X-RAY DIFFRACTION	18	{ L\|* }
19	X-RAY DIFFRACTION	19	{ N\|* }
20	X-RAY DIFFRACTION	20	{ P\|* }
21	X-RAY DIFFRACTION	21	{ R\|* }
22	X-RAY DIFFRACTION	22	{ T\|* }
23	X-RAY DIFFRACTION	23	{ V\|* }
24	X-RAY DIFFRACTION	24	{ X\|* }

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