PDB-8ah9: De novo retro-aldolase RAbetaB-16.1

ID or keywords:

Entry

Database: PDB / ID: 8ah9

Title

De novo retro-aldolase RAbetaB-16.1

Components

RAbetaB-16.1

Keywords

DE NOVO PROTEIN / retro-aldolase / beta-barrel

Function / homology

BENZOIC ACID

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.747 Å

Authors

Mittl, P. / Oualb Chaib, A. / Hilvert, D.

Funding support

1items

Citation

Journal: Protein Sci. / Year: 2022
Title: Design and optimization of enzymatic activity in a de novo beta-barrel scaffold.
Authors: Kipnis, Y. / Chaib, A.O. / Vorobieva, A.A. / Cai, G. / Reggiano, G. / Basanta, B. / Kumar, E. / Mittl, P.R.E. / Hilvert, D. / Baker, D.

History

Deposition	Jul 21, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ah9.cif.gz	79.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8ah9.ent.gz	45.9 KB	Display	PDB format
PDBx/mmJSON format	8ah9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ah9_validation.pdf.gz	438.8 KB	Display	wwPDB validaton report
Full document	8ah9_full_validation.pdf.gz	440.1 KB	Display
Data in XML	8ah9_validation.xml.gz	7.8 KB	Display
Data in CIF	8ah9_validation.cif.gz	10.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ah/8ah9 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ah9	HTTPS FTP

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Related structure data

Related structure data	6czgS 6czjS 6d0tS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: RAbetaB-16.1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	55.482, 77.485, 60.652
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	RAbetaB-16.1 Mass: 13881.747 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-BEZ / BENZOIC ACID Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.35 Å³/Da / Density % sol: 47.61 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 0.1 M Bis-TRIS, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 13, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.737→45.11 Å / Num. obs: 13587 / % possible obs: 99.96 % / Redundancy: 2 % / B_iso Wilson estimate: 24.72 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.024 / R_pim(I) all: 0.024 / R_rim(I) all: 0.034 / Net I/σ(I): 17.82
Reflection shell	Resolution: 1.75→1.81 Å / Num. unique obs: 1326 / CC_1/2: 0.565 / R_pim(I) all: 0.565

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0349	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6czg,6czj, 6d0t

6czg

6czj

6d0t

Resolution: 1.747→45.11 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.951 / SU B: 6.12 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2257	677	4.983 %
R_work	0.1865	12910	-
all	0.188	-	-
obs	-	13587	99.904 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.287 Å²	0 Å²	-0 Å²
2-	-	0.341 Å²	0 Å²
3-	-	-	-0.629 Å²

Refinement step

Cycle: LAST / Resolution: 1.747→45.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	925	0	27	70	1022

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	1016
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	926
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	1.667	1369
X-RAY DIFFRACTION	r_angle_other_deg	0.493	1.566	2169
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.988	5	124
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.38	10	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.93	10	186
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.403	10	45
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	136
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1197
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	219
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	136
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	830
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	441
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	563
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.303	0.2	52
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.185	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.159	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.109	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	2.663	2.228	484
X-RAY DIFFRACTION	r_mcbond_other	2.272	2.227	484
X-RAY DIFFRACTION	r_mcangle_it	3.453	3.328	612
X-RAY DIFFRACTION	r_mcangle_other	3.453	3.333	613
X-RAY DIFFRACTION	r_scbond_it	5.683	3.302	532
X-RAY DIFFRACTION	r_scbond_other	5.678	3.304	533
X-RAY DIFFRACTION	r_scangle_it	9.265	4.613	757
X-RAY DIFFRACTION	r_scangle_other	9.26	4.615	758
X-RAY DIFFRACTION	r_lrange_it	11.631	36.545	1057
X-RAY DIFFRACTION	r_lrange_other	11.625	36.539	1058

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.747-1.793	0.393	51	0.311	932	0.315	993	0.902	0.931	98.993	0.304
1.793-1.842	0.337	52	0.295	912	0.298	964	0.934	0.941	100	0.282
1.842-1.895	0.263	42	0.282	888	0.281	930	0.958	0.947	100	0.255
1.895-1.953	0.259	49	0.212	859	0.215	908	0.956	0.968	100	0.183
1.953-2.017	0.211	50	0.189	834	0.19	884	0.972	0.975	100	0.157
2.017-2.088	0.221	42	0.177	831	0.179	873	0.972	0.98	100	0.149
2.088-2.166	0.197	42	0.162	779	0.164	821	0.98	0.984	100	0.137
2.166-2.255	0.238	30	0.173	757	0.175	787	0.966	0.981	100	0.149
2.255-2.355	0.25	36	0.185	739	0.189	775	0.952	0.978	100	0.156
2.355-2.469	0.228	36	0.181	688	0.184	724	0.971	0.981	100	0.152
2.469-2.602	0.214	34	0.172	666	0.174	700	0.975	0.983	100	0.143
2.602-2.76	0.205	32	0.169	647	0.17	679	0.976	0.981	100	0.147
2.76-2.949	0.194	32	0.172	582	0.173	614	0.971	0.981	100	0.147
2.949-3.185	0.2	32	0.177	571	0.178	603	0.975	0.98	100	0.161
3.185-3.487	0.214	21	0.193	506	0.194	527	0.972	0.978	100	0.182
3.487-3.895	0.212	28	0.168	474	0.17	502	0.977	0.982	100	0.162
3.895-4.492	0.193	22	0.148	415	0.15	437	0.984	0.987	100	0.145
4.492-5.488	0.24	18	0.174	370	0.177	388	0.975	0.985	100	0.176
5.488-7.705	0.255	15	0.224	284	0.225	299	0.977	0.966	100	0.217
7.705-45.11	0.25	13	0.231	176	0.232	189	0.947	0.952	100	0.234

Refinement TLS params.

Method: refined / Origin x: 17.2908 Å / Origin y: 24.5561 Å / Origin z: 29.3497 Å

	11	12	13	21	22	23	31	32	33
T	0.0222 Å²	-0.0016 Å²	-0.0048 Å²	-	0.024 Å²	0.0092 Å²	-	-	0.005 Å²
L	0.5629 °²	0.1245 °²	-0.2373 °²	-	0.4104 °²	0.2683 °²	-	-	0.3689 °²
S	-0.0006 Å °	-0.0197 Å °	0.0023 Å °	-0.0191 Å °	-0.0089 Å °	0.0172 Å °	-0.0194 Å °	0.0097 Å °	0.0095 Å °

Refinement TLS group

Selection: ALL

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