PDB-7rbw: Structure of Biliverdin-binding Serpin of Boana punctata (polka-d...

ID or keywords:

Entry

Database: PDB / ID: 7rbw

Title

Structure of Biliverdin-binding Serpin of Boana punctata (polka-dot tree frog)

Components

Biliverdin bindin serpin

Keywords

FLUORESCENT PROTEIN / Serpin / Biliverdin-binding serpin / Near-infrared

Function / homology

Function and homology information

serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function

Biological species

Boana punctata (polka-dot treefrog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.05 Å

Authors

Fedorov, E. / Manoilov, K.Y. / Verkhusha, V. / Almo, S.C. / Ghosh, A.

Funding support

United States, 1items

Citation

Journal: J.Mol.Biol. / Year: 2021
Title: Structural and Functional Characterization of a Biliverdin-Binding Near-Infrared Fluorescent Protein From the Serpin Superfamily.
Authors: Manoilov, K.Y. / Ghosh, A. / Almo, S.C. / Verkhusha, V.V.

History

Deposition	Jul 6, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 1, 2021	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Dec 8, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7rbw.cif.gz	325.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7rbw.ent.gz	264.9 KB	Display	PDB format
PDBx/mmJSON format	7rbw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7rbw_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7rbw_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7rbw_validation.xml.gz	30 KB	Display
Data in CIF	7rbw_validation.cif.gz	40.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rb/7rbw ftp://data.pdbj.org/pub/pdb/validation_reports/rb/7rbw	HTTPS FTP

-
Related structure data

Related structure data	5nbuS 1atu S: Starting model for refinement
Similar structure data	7rbw-2 7b62-d 3zdb-d 7pmu-d 1ey2-d 1eyb-d 2p3f-d 4iyp-d 6fk6-d 6lqo-5 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#53 - May 2004 Serpins similarity (8)

Deposited unit

A: Biliverdin bindin serpin

B: Biliverdin bindin serpin

hetero molecules

95.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Biliverdin bindin serpin

hetero molecules

defined by author&software
Evidence: gel filtration, Superdex S200
47.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Biliverdin bindin serpin

hetero molecules

defined by author&software
47.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.069, 75.910, 143.751
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Biliverdin bindin serpin Mass: 47328.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Boana punctata (polka-dot treefrog) / Gene: BBS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7D7FB99
#2: Chemical	ChemComp-BLA / BILIVERDINE IX ALPHA Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₃H₃₄N₄O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.78 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M Ammonium nitrate, 20% w/v Polyethylene glycol 3,350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2020 / Details: KB MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.05→19.97 Å / Num. obs: 50138 / % possible obs: 99.8 % / Redundancy: 12.8 % / B_iso Wilson estimate: 37.51 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 18.2
Reflection shell	Resolution: 2.05→2.11 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.725 / % possible all: 99.9

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4.53 Å	19.97 Å
Translation	4.53 Å	19.97 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.1_4122	refinement
MOSFLM		data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NBU

5nbu

Resolution: 2.05→19.97 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.237	2481	4.95 %
R_work	0.199	-	-
obs	0.201	50072	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→19.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6147	0	86	134	6367

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.09	0.2729	128	0.2463	2595	X-RAY DIFFRACTION	100
2.09-2.13	0.2802	140	0.247	2609	X-RAY DIFFRACTION	100
2.13-2.18	0.3144	122	0.244	2630	X-RAY DIFFRACTION	100
2.18-2.23	0.303	127	0.2328	2628	X-RAY DIFFRACTION	100
2.23-2.28	0.2874	123	0.2447	2611	X-RAY DIFFRACTION	100
2.28-2.35	0.267	155	0.2408	2577	X-RAY DIFFRACTION	100
2.35-2.42	0.2489	137	0.2329	2620	X-RAY DIFFRACTION	100
2.42-2.49	0.2713	139	0.2462	2639	X-RAY DIFFRACTION	100
2.49-2.58	0.2796	132	0.2446	2625	X-RAY DIFFRACTION	100
2.58-2.69	0.2664	134	0.2366	2641	X-RAY DIFFRACTION	100
2.69-2.81	0.2757	133	0.2443	2631	X-RAY DIFFRACTION	100
2.81-2.95	0.2793	183	0.2327	2585	X-RAY DIFFRACTION	100
2.95-3.14	0.2952	173	0.2326	2624	X-RAY DIFFRACTION	100
3.14-3.38	0.2276	136	0.2202	2641	X-RAY DIFFRACTION	100
3.38-3.72	0.25	109	0.195	2695	X-RAY DIFFRACTION	100
3.72-4.25	0.1959	141	0.1717	2701	X-RAY DIFFRACTION	100
4.25-5.34	0.2013	128	0.1476	2696	X-RAY DIFFRACTION	99
5.34-19.97	0.19	141	0.1651	2843	X-RAY DIFFRACTION	99

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	3.6138	-5.036	-0.6266	4.3705	0.1195	-0.0618	-0.4315	-0.3882	0.0916	0.4754	0.6681	-0.3543	-0.073	-0.068	-0.1251	0.549	0.0051	-0.1323	0.5038	-0.0114	0.3585	28.2306	30.2154	-15.0613
2	2.4808	-1.6828	1.8206	2.5062	-1.4185	2.924	0.2493	0.1163	-0.3901	-0.2129	-0.0143	0.2357	0.452	0.0345	-0.2454	0.3861	0.0271	-0.0259	0.2742	0.0452	0.3707	21.8625	-6.6423	-11.477
3	3.0302	-0.202	-0.3626	4.792	0.8738	3.78	0.0578	-0.1131	-0.0927	0.3659	0.1018	-0.384	0.2732	0.3198	-0.0704	0.3299	0.0737	-0.1023	0.3295	0.0444	0.3987	31.5187	-8.7059	-1.3752
4	5.5672	-0.8504	0.5592	4.9662	0.2922	3.4556	0.2331	-0.716	-0.0469	1.1661	-0.1381	0.6019	1.0498	-0.429	-0.0888	0.845	-0.1263	-0.0066	0.3886	0.0264	0.4358	20.6661	-13.8213	8.7004
5	0.9158	-0.9261	0.2474	3.2253	-0.4482	2.5781	-0.0315	0.0382	-0.1847	0.0002	0.1027	0.422	-0.0602	-0.2888	-0.0807	0.2183	0.005	-0.0067	0.2723	0.0618	0.3639	12.0807	8.4081	-11.0426
6	3.8626	-1.5162	0.147	4.3992	0.8545	3.3201	0.3684	0.2042	-0.9341	0.1262	-0.0907	0.3131	0.8313	0.1953	-0.3036	0.4744	-0.0059	-0.0994	0.3099	-0.0087	0.488	22.9645	-19.5885	-5.7917
7	0.6653	-1.5917	0.9872	3.8847	-1.3934	1.4947	-0.1287	-0.0964	-0.1074	0.2611	0.3202	0.5324	-0.2879	-0.2572	-0.2163	0.2853	0.052	0.0295	0.3102	0.0827	0.3458	12.5309	7.5951	-8.005
8	2.3339	1.8659	0.6946	1.4711	0.0614	0.4086	-0.1621	0.4203	-0.2359	-0.6101	0.4355	-0.4643	0.4405	-0.0009	-0.2595	0.5286	0.1328	0.0492	0.5218	-0.1124	0.4582	21.925	-61.7976	-33.5462
9	3.5517	0.9091	-1.7412	2.0401	-1.5194	4.0896	0.0721	0.0241	0.0774	-0.0242	-0.0685	-0.0633	-0.0183	0.3931	0.0132	0.2934	0.0395	-0.0143	0.3259	0.0378	0.2821	26.9531	-25.5052	-41.6727
10	4.7018	0.6981	-0.7256	3.2085	-1.9967	5.6066	0.147	0.7014	0.8125	0.0698	0.3617	0.582	-0.4042	-0.6342	-0.4046	0.4103	0.1008	0.0348	0.5129	0.1473	0.4929	17.5357	-14.8795	-52.0249
11	1.5126	0.4244	-0.6066	2.4463	-1.1118	2.3839	0.0012	0.057	0.1346	-0.0525	0.2111	0.2769	0.0377	-0.1103	-0.2275	0.2725	0.0457	-0.0164	0.2791	0.0295	0.2583	13.412	-34.1927	-32.6052

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 28 THROUGH 50 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 51 THROUGH 93 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 94 THROUGH 153 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 154 THROUGH 200 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 201 THROUGH 314 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 315 THROUGH 352 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 353 THROUGH 417 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 29 THROUGH 50 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 51 THROUGH 147 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 148 THROUGH 217 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 218 THROUGH 417 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi