PDB-4w6p: Crystal Structure of Full-Length Split GFP Mutant D102C Disulfide...

ID or keywords:

Entry

Database: PDB / ID: 4w6p

Title

Crystal Structure of Full-Length Split GFP Mutant D102C Disulfide Dimer, P 21 21 21 Space Group

Components

fluorescent protein D102C

Keywords

FLUORESCENT PROTEIN / dimer / disulfide

Function / homology

Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.085 Å

Authors

Leibly, D.J. / Waldo, G.S. / Yeates, T.O.

Funding support

United States, 1items

Citation

Journal: Structure / Year: 2015
Title: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding.
Authors: Leibly, D.J. / Arbing, M.A. / Pashkov, I. / DeVore, N. / Waldo, G.S. / Terwilliger, T.C. / Yeates, T.O.

History

Deposition	Aug 20, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4w6p.cif.gz	654.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4w6p.ent.gz	550.4 KB	Display	PDB format
PDBx/mmJSON format	4w6p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4w6p_validation.pdf.gz	499.2 KB	Display	wwPDB validaton report
Full document	4w6p_full_validation.pdf.gz	539.5 KB	Display
Data in XML	4w6p_validation.xml.gz	61.9 KB	Display
Data in CIF	4w6p_validation.cif.gz	79.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/4w6p ftp://data.pdbj.org/pub/pdb/validation_reports/w6/4w6p	HTTPS FTP

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Related structure data

Related structure data	4w69C 4w6aC 4w6bC 4w6cC 4w6dC 4w6fC 4w6gC 4w6hC 4w6iC 4w6jC 4w6kC 4w6lC 4w6mC 4w6nC 4w6oC 4w6rC 4w6sC 4w6tC 4w6uC 4w72C 4w73C 4w74C 4w75C 4w76C 4w77C 4w7aC 4w7cC 4w7dC 4w7eC 4w7fC 4w7rC 4w7xC 2b3pS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4w6r-5 4j1v-d 4w6r-2 6q6j-d 6srr-d 5yel-1 3huh-d 2ztn-d 6czo-d 4w6r-6 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 - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: fluorescent protein D102C

B: fluorescent protein D102C

C: fluorescent protein D102C

D: fluorescent protein D102C

E: fluorescent protein D102C

F: fluorescent protein D102C

G: fluorescent protein D102C

H: fluorescent protein D102C

215 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: fluorescent protein D102C

B: fluorescent protein D102C

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

2

C: fluorescent protein D102C

D: fluorescent protein D102C

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

3

E: fluorescent protein D102C

H: fluorescent protein D102C

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

4

F: fluorescent protein D102C

G: fluorescent protein D102C

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

Unit cell

Length a, b, c (Å)	86.050, 117.860, 209.100
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	fluorescent protein D102C Mass: 26816.193 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
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: 2.47 Å³/Da / Density % sol: 50.23 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.3M NaNO3, 0.1M NaAcetate pH 5.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 9, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 3.085→79.58 Å / Num. obs: 39143 / % possible obs: 98 % / Redundancy: 6.7 % / R_sym value: 0.1491 / Net I/σ(I): 10.85

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p

Resolution: 3.085→79.575 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2789	3914	10 %
R_work	0.2323	-	-
obs	0.237	39137	97.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.085→79.575 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12960	0	0	0	12960

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	13217
X-RAY DIFFRACTION	f_angle_d	1.414	17836
X-RAY DIFFRACTION	f_dihedral_angle_d	14.73	4844
X-RAY DIFFRACTION	f_chiral_restr	0.054	1976
X-RAY DIFFRACTION	f_plane_restr	0.007	2277

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 (%)
3.0852-3.1228	0.4499	98	0.3755	874	X-RAY DIFFRACTION	71
3.1228-3.1624	0.3233	141	0.293	1274	X-RAY DIFFRACTION	100
3.1624-3.204	0.3462	140	0.297	1259	X-RAY DIFFRACTION	98
3.204-3.2479	0.3585	138	0.2833	1238	X-RAY DIFFRACTION	100
3.2479-3.2943	0.3333	139	0.2724	1259	X-RAY DIFFRACTION	100
3.2943-3.3435	0.3509	139	0.2693	1249	X-RAY DIFFRACTION	99
3.3435-3.3957	0.307	142	0.2764	1276	X-RAY DIFFRACTION	100
3.3957-3.4514	0.3189	134	0.2753	1210	X-RAY DIFFRACTION	96
3.4514-3.5109	0.3421	137	0.2729	1227	X-RAY DIFFRACTION	98
3.5109-3.5747	0.3404	142	0.2511	1277	X-RAY DIFFRACTION	99
3.5747-3.6435	0.3339	140	0.2464	1262	X-RAY DIFFRACTION	99
3.6435-3.7179	0.297	139	0.245	1253	X-RAY DIFFRACTION	100
3.7179-3.7987	0.2682	141	0.2332	1270	X-RAY DIFFRACTION	99
3.7987-3.8871	0.2915	141	0.2264	1267	X-RAY DIFFRACTION	100
3.8871-3.9843	0.3089	141	0.223	1268	X-RAY DIFFRACTION	99
3.9843-4.092	0.2477	142	0.217	1279	X-RAY DIFFRACTION	100
4.092-4.2124	0.231	140	0.2079	1256	X-RAY DIFFRACTION	100
4.2124-4.3483	0.2424	142	0.2007	1276	X-RAY DIFFRACTION	99
4.3483-4.5037	0.2029	140	0.1919	1268	X-RAY DIFFRACTION	100
4.5037-4.684	0.234	136	0.18	1217	X-RAY DIFFRACTION	95
4.684-4.8972	0.2492	144	0.1896	1295	X-RAY DIFFRACTION	100
4.8972-5.1553	0.2169	140	0.1797	1270	X-RAY DIFFRACTION	100
5.1553-5.4783	0.2438	143	0.2017	1288	X-RAY DIFFRACTION	100
5.4783-5.9011	0.2392	145	0.2186	1310	X-RAY DIFFRACTION	100
5.9011-6.4947	0.2893	145	0.2416	1298	X-RAY DIFFRACTION	100
6.4947-7.4339	0.3299	142	0.26	1277	X-RAY DIFFRACTION	97
7.4339-9.3636	0.2683	147	0.2365	1332	X-RAY DIFFRACTION	100
9.3636-79.6017	0.305	156	0.2674	1394	X-RAY DIFFRACTION	98

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	3.3527	-0.1016	0.237	3.5408	-0.9257	3.7028	-0.0575	0.1145	0.0058	-0.0874	0.1318	0.0552	0.0977	-0.1589	-0.0576	0.3896	0.0235	0.0216	0.3374	0.0705	0.4844	32.7872	10.7477	45.779
2	3.4673	-0.0645	-0.1737	3.6673	0.1944	3.9725	0.0682	0.2889	-0.2388	-0.3947	-0.1768	-0.0863	0.3718	0.2337	0.0677	0.4528	0.0962	0.0712	0.4676	0.0838	0.5624	65.4231	34.5012	25.1271
3	4.508	-0.7237	1.095	6.0306	-0.3396	4.0871	0.1059	0.3707	-0.1126	-0.8774	-0.1238	0.1711	0.2447	0.1232	-0.0128	0.4528	0.0364	0.0061	0.4197	0.0862	0.4533	29.4381	42.0825	23.4843
4	3.0523	-0.3378	0.4704	5.6223	-1.791	4.5765	-0.0612	0.3901	0.5509	0.2521	-0.0079	-0.1472	-0.4753	0.4621	0.0284	0.395	-0.0265	0.0677	0.4784	0.1369	0.5654	62.0103	72.2875	20.0942
5	3.4568	-0.091	-0.1505	3.4992	-0.5647	4.2873	-0.0239	0.2656	0.3462	0.031	-0.1395	0.0982	-0.4855	0.5481	0.2061	0.4833	-0.0089	-0.1309	0.5625	0.2386	0.7228	9.1798	63.3806	20.1585
6	3.9529	0.5775	-0.3594	4.4036	-0.4785	4.0701	0.1182	-0.1002	-0.7111	0.1149	-0.3329	0.0532	0.2587	0.2369	0.1776	0.4347	0.0672	0.007	0.5211	0.0801	0.9041	-0.0507	17.4679	39.2095
7	3.7009	-0.6859	1.2641	3.5984	-0.0218	4.1166	-0.0204	0.0757	-0.435	-0.4886	-0.0844	-0.1601	0.2423	-0.1027	0.1226	0.6837	0.0224	0.074	0.3916	0.0001	0.6951	-36.2221	-7.3836	30.2362
8	0.7971	-0.2692	0.3551	1.6321	-0.8793	3.0248	0.0927	1.2137	1.1297	-0.4978	0.353	0.7087	0.0556	-0.6449	-0.3341	0.7705	0.0403	0.0144	1.3498	0.7	1.0537	45.167	77.8515	-1.484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESSEQ 4:229)
2	X-RAY DIFFRACTION	2	(CHAIN B AND RESSEQ 4:226)
3	X-RAY DIFFRACTION	3	(CHAIN C AND RESSEQ 5:227)
4	X-RAY DIFFRACTION	4	(CHAIN D AND RESSEQ 4:229)
5	X-RAY DIFFRACTION	5	(CHAIN E AND RESSEQ 4:227)
6	X-RAY DIFFRACTION	6	(CHAIN F AND RESSEQ 4:228)
7	X-RAY DIFFRACTION	7	(CHAIN G AND RESSEQ 4:226)
8	X-RAY DIFFRACTION	8	(CHAIN H AND RESSEQ 10:225)

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