PDB-4pej: Crystal structure of a computationally designed retro-aldolase, R...

ID or keywords:

Entry

Database: PDB / ID: 4pej

Title

Crystal structure of a computationally designed retro-aldolase, RA110.4 (Cys free)

Components

Retro-aldolase

Keywords

LYASE / computationally designed enzyme / fluorescent probe

Function / homology

Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta

Function and homology information

Biological species

ARTIFICIAL GENE (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Bhabha, G. / Zhang, X. / Liu, Y. / Ekiert, D.C.

Citation

Journal: J.Am.Chem.Soc. / Year: 2014
Title: De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters.
Authors: Liu, Y. / Zhang, X. / Tan, Y.L. / Bhabha, G. / Ekiert, D.C. / Kipnis, Y. / Bjelic, S. / Baker, D. / Kelly, J.W.

History

Deposition	Apr 23, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4pej.cif.gz	115.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4pej.ent.gz	90.5 KB	Display	PDB format
PDBx/mmJSON format	4pej.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4pej_validation.pdf.gz	435 KB	Display	wwPDB validaton report
Full document	4pej_full_validation.pdf.gz	435.8 KB	Display
Data in XML	4pej_validation.xml.gz	11 KB	Display
Data in CIF	4pej_validation.cif.gz	14 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/4pej ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pej	HTTPS FTP

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Related structure data

Related structure data	4pekC 1w02S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ul3-1 5uwg-1 4i1k-1 1e97-d 1c7h-d 6bs9-2 6qqi-d 6f4y-1 6c17-d 5cm4-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Retro-aldolase

B: Retro-aldolase

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

1

A: Retro-aldolase

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

2

B: Retro-aldolase

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

Unit cell

Length a, b, c (Å)	35.490, 74.160, 94.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Retro-aldolase Mass: 16000.956 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARTIFICIAL GENE (others) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 36.96 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate, pH 4.5 and 40% (v/v) PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.12 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 21967 / % possible obs: 99.1 % / Redundancy: 6.8 % / Net I/σ(I): 1.5

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Processing

Software

Name: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1W02

1w02

Resolution: 1.85→39.966 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2377	1099	5.01 %
R_work	0.2115	-	-
obs	0.2127	21954	99.08 %

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→39.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1946	0	0	37	1983

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2037
X-RAY DIFFRACTION	f_angle_d	1.019	2771
X-RAY DIFFRACTION	f_dihedral_angle_d	13.062	753
X-RAY DIFFRACTION	f_chiral_restr	0.038	296
X-RAY DIFFRACTION	f_plane_restr	0.005	367

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 (%)
1.85-1.9333	0.3351	130	0.3004	2454	X-RAY DIFFRACTION	95
1.9333-2.0352	0.3064	135	0.2755	2575	X-RAY DIFFRACTION	100
2.0352-2.1627	0.2643	138	0.2493	2607	X-RAY DIFFRACTION	100
2.1627-2.3297	0.2521	136	0.2323	2587	X-RAY DIFFRACTION	100
2.3297-2.5641	0.2225	137	0.2294	2616	X-RAY DIFFRACTION	100
2.5641-2.935	0.2532	138	0.2289	2610	X-RAY DIFFRACTION	100
2.935-3.6974	0.2162	139	0.2027	2654	X-RAY DIFFRACTION	100
3.6974-39.9751	0.225	146	0.1822	2752	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	0.3211	-0.3248	0.0991	0.5777	0.6902	0.9141	0.0074	0.027	-0.2978	0.1899	-0.0891	-0.3031	0.5092	0.009	0.0003	0.3442	-0.0549	-0.0297	0.3051	-0.0104	0.2861	-2.7361	233.0362	58.7835
2	0.4071	-0.1831	0.9245	1.381	-1.1733	1.3845	0.3135	0.1681	-0.0256	-0.0455	-0.1977	-0.1555	-0.6222	-0.0291	0.0213	0.1997	-0.0124	-0.0026	0.3846	-0.0177	0.2394	-10.6591	241.3648	53.8827
3	0.1023	0.0046	-0.0521	0.2898	-0.3725	0.5528	0.4354	-0.1237	0.1087	-0.0546	-0.1445	-0.1837	-1.6972	-0.7892	0.0242	0.4332	0.0658	-0.0623	0.5283	-0.0561	0.4851	-15.6933	251.0786	59.9392
4	0.4919	0.1209	0.1795	0.2804	-0.1085	0.1026	-0.1069	0.2197	0.1999	-0.0263	0.1111	-0.2739	0.0329	-0.2169	0.01	0.1838	-0.038	-0.0691	0.3111	-0.0092	0.2886	-9.786	247.9729	50.8685
5	0.2008	0.3626	0.4979	0.3977	-0.6681	0.4444	0.121	-0.0572	0.0769	-0.0023	0.1399	-0.173	0.4525	-0.0356	0.3243	0.2315	0.01	0.0295	0.2612	0.0011	0.372	-0.0728	239.0078	63.4588
6	0.2947	-0.9351	-1.0202	2.1783	0.8891	1.689	0.451	-0.2192	0.2117	-0.7737	0.2776	-0.6372	0.0766	-0.1364	0.3443	0.3229	0.0362	0.1973	0.1503	-0.0974	0.4319	3.6071	247.4558	63.1779
7	0.6481	-0.2246	0.335	1.1122	-0.2935	0.6024	-0.0754	0.0486	-0.2929	-0.7406	0.1351	-0.5193	0.0145	-0.2129	0.1076	0.2016	-0.0223	0.0225	0.2651	0.0184	0.2987	-4.4687	242.9478	64.7836
8	0.0116	-0.2007	0.4096	0.3695	-0.5004	0.5245	0.1146	-0.0941	0.0489	-0.1873	-0.1227	0.0429	0.085	-0.5834	-0.0024	0.2583	-0.0194	-0.0356	0.3403	0.0085	0.3187	-13.0359	237.5285	60.5725
9	0.891	0.3577	0.206	1.1099	-0.9773	2.4021	0.3459	-0.3813	0.8365	0.065	0.2425	0.3713	-0.8042	-0.0455	0.2133	0.3755	-0.0423	0.0927	0.2607	-0.0691	0.4918	1.9423	255.2663	67.7164
10	1.335	0.4344	-0.122	0.0634	-0.3216	0.4091	0.4809	-0.1217	0.028	0.2813	-0.078	0.2337	-0.2657	-0.0304	0.0407	0.6064	0.0726	-0.0449	0.3174	-0.0237	0.3281	-4.6517	249.2263	83.3005
11	0.2032	-0.1878	-0.4025	1.2715	0.5033	1.1933	0.2487	-0.004	0.1542	0.7139	-0.3889	0.3524	0.4274	-0.7119	-0.3814	0.8012	0.0022	0.2199	0.4978	-0.0202	0.3499	-13.6779	241.9068	88.3751
12	0.0037	-0.1749	-0.0864	0.1706	0.0434	0.1761	0.3789	0.0248	0.096	0.24	-0.3404	-0.42	0.4066	-0.5689	0.0145	0.6895	-0.1454	0.2134	0.606	0.0092	0.4973	-17.0346	231.8271	79.1223
13	2.8222	1.7937	2.4677	1.456	0.8507	2.9002	-0.3136	0.8218	-0.631	0.676	0.232	-0.4806	1.7772	-0.6638	1.2386	0.8693	-0.0952	0.2374	0.4846	0.0045	0.3498	-13.5074	234.0964	90.6806
14	0.6403	0.3779	0.0283	0.4654	0.9465	1.6291	-0.0117	-0.2152	-0.0302	0.5869	0.069	-0.1118	0.2842	-0.001	-0	0.4146	0.0251	-0.0609	0.3003	0.0458	0.3101	-0.3454	238.1342	81.0617
15	0.2738	0.029	-0.503	0.2233	-0.4803	0.1588	-0.2435	-0.2234	-0.2938	0.6513	0.2613	0.0646	-0.0562	-0.2075	0.0175	0.5131	0.1158	-0.0307	0.3071	-0.0006	0.2878	-3.6145	236.4856	78.8495
16	1.4007	-0.1617	0.9329	0.8258	-0.6829	0.6439	0.3402	-0.0322	-0.2449	0.2803	-0.2892	0.2879	0.1375	-0.435	0.0467	0.4279	0.0339	0.0894	0.2986	0.02	0.2869	-9.4733	238.4523	78.7254

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 42 through 49 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 50 through 60 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 80 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 81 through 96 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 97 through 107 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 108 through 119 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 120 through 128 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 22 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 23 through 39 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 40 through 49 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 50 through 61 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 62 through 94 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 95 through 107 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 108 through 127 )

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