PDB-5c5y: Crystal structure of deoxyribose-phosphate aldolase from Colwelli...

ID or keywords:

Entry

Database: PDB / ID: 5c5y

Title

Crystal structure of deoxyribose-phosphate aldolase from Colwellia psychrerythraea (hexagonal form)

Components

Deoxyribose-phosphate aldolase

Keywords

LYASE / DERA /

TIM barrel /

psychrophilic

Function / homology

Function and homology information

deoxyribose-phosphate aldolase /

deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process /

cytoplasm
Similarity search - Function

Biological species

Colwellia psychrerythraea (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Weiergraeber, O.H. / Dick, M. / Pietruszka, J.

Citation

Journal: Sci Rep / Year: 2016
Title: Trading off stability against activity in extremophilic aldolases.
Authors: Dick, M. / Weiergraber, O.H. / Classen, T. / Bisterfeld, C. / Bramski, J. / Gohlke, H. / Pietruszka, J.

History

Deposition	Jun 22, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5c5y.cif.gz	386 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/5c5y ftp://data.pdbj.org/pub/pdb/validation_reports/c5/5c5y	HTTPS FTP

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Related structure data

Related structure data	5c2xSC 5c6mC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3npv-d 5c6m-1 6z9j-d 1ktn-d 1jcl-d 6z9h-d 1p1x-d 5c2x-d 3q2d-d 2bhd-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (3) #137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Deoxyribose-phosphate aldolase

B: Deoxyribose-phosphate aldolase

C: Deoxyribose-phosphate aldolase

D: Deoxyribose-phosphate aldolase

hetero molecules

114 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Deoxyribose-phosphate aldolase

B: Deoxyribose-phosphate aldolase

hetero molecules

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

2

C: Deoxyribose-phosphate aldolase

D: Deoxyribose-phosphate aldolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.840, 115.840, 400.100
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	B-515- HOH
2	1	B-519- HOH
3	1	B-520- HOH

#1: Protein	Deoxyribose-phosphate aldolase / Mass: 28330.271 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria) Gene: deoC, CPS_1972 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q483R4, deoxyribose-phosphate aldolase
#2: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 438 / 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	Density Matthews: 3.67 Å³/Da / Density % sol: 66.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 1000, calcium acetate, imidazole, triethanolamine

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.969 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.969 Å / Relative weight: 1

Reflection

Resolution: 2.1→49.77 Å / Num. obs: 93159 / % possible obs: 99.6 % / Redundancy: 13.4 % / B_iso Wilson estimate: 36.38 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.087 / R_rim(I) all: 0.091 / Χ²: 0.963 / Net I/σ(I): 21.4 / Num. measured all: 1250142

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.1-2.15		12.8	0.875	1.142	2.62	85783	6775	6628	1.188	97.8
2.15-2.21			0.945	0.841	3.91	92430	6598	6557	0.872	99.4
2.21-2.28			0.966	0.676	4.74	89773	6479	6445	0.702	99.5
2.28-2.35			0.973	0.554	5.59	85406	6238	6208	0.575	99.5
2.35-2.42			0.983	0.449	6.53	81214	6108	6081	0.466	99.6
2.42-2.51			0.982	0.353	7.84	75598	5892	5873	0.368	99.7
2.51-2.6			0.992	0.278	10.34	79619	5671	5652	0.288	99.7
2.6-2.71			0.995	0.218	12.54	76619	5523	5510	0.227	99.8
2.71-2.83			0.997	0.162	15.96	71961	5275	5267	0.169	99.8
2.83-2.97			0.997	0.128	19.2	66401	5067	5059	0.134	99.8
2.97-3.13			0.998	0.106	22.63	63225	4837	4834	0.11	99.9
3.13-3.32			0.999	0.081	29.78	63342	4556	4554	0.084	100
3.32-3.55			0.999	0.067	35.33	58868	4307	4303	0.069	99.9
3.55-3.83			0.999	0.051	43.73	53463	4046	4045	0.053	100
3.83-4.2			0.999	0.044	49.99	48132	3756	3753	0.046	99.9
4.2-4.7			1	0.039	58.19	46357	3397	3397	0.04	100
4.7-5.42			0.999	0.038	58.07	39919	3051	3050	0.039	100
5.42-6.64			0.999	0.041	52.07	32068	2615	2614	0.043	100
6.64-9.39			1	0.032	64.88	26311	2078	2078	0.033	100
	9.39		0.999	0.031	66.86	13653	1272	1251	0.033	98.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Classification
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
XDS	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5C2X

5c2x

Resolution: 2.1→49.77 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 21.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1989	4657	5 %	random selection
R_work	0.1727	88448	-	-
obs	0.1741	93105	99.55 %	-

Solvent computation

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

Displacement parameters

B_iso max: 134.34 Å² / B_iso mean: 50.4361 Å² / B_iso min: 22.8 Å²

Refinement step

Cycle: final / Resolution: 2.1→49.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7308	0	48	438	7794
B_iso mean	-	-	69.28	48.51	-
Num. residues	-	-	-	-	986

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7540
X-RAY DIFFRACTION	f_angle_d	0.903	10237
X-RAY DIFFRACTION	f_chiral_restr	0.036	1239
X-RAY DIFFRACTION	f_plane_restr	0.005	1331
X-RAY DIFFRACTION	f_dihedral_angle_d	11.579	2731

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 (%)
2.0999-2.1238	0.2778	146	0.2638	2776	X-RAY DIFFRACTION	97
2.1238-2.1488	0.2996	152	0.2356	2890	X-RAY DIFFRACTION	98
2.1488-2.175	0.2788	151	0.226	2866	X-RAY DIFFRACTION	99
2.175-2.2025	0.2152	152	0.2106	2876	X-RAY DIFFRACTION	99
2.2025-2.2315	0.2497	154	0.2125	2922	X-RAY DIFFRACTION	99
2.2315-2.2621	0.2201	149	0.1992	2843	X-RAY DIFFRACTION	99
2.2621-2.2944	0.2604	153	0.2048	2898	X-RAY DIFFRACTION	99
2.2944-2.3287	0.2391	153	0.2044	2904	X-RAY DIFFRACTION	99
2.3287-2.365	0.2467	154	0.201	2920	X-RAY DIFFRACTION	100
2.365-2.4038	0.2406	152	0.1965	2885	X-RAY DIFFRACTION	100
2.4038-2.4453	0.2341	153	0.2067	2915	X-RAY DIFFRACTION	100
2.4453-2.4897	0.2586	153	0.2018	2899	X-RAY DIFFRACTION	100
2.4897-2.5376	0.2437	154	0.187	2925	X-RAY DIFFRACTION	100
2.5376-2.5894	0.2199	153	0.1792	2912	X-RAY DIFFRACTION	100
2.5894-2.6457	0.2311	155	0.1834	2927	X-RAY DIFFRACTION	100
2.6457-2.7072	0.2157	154	0.1862	2920	X-RAY DIFFRACTION	100
2.7072-2.7749	0.1835	153	0.1826	2923	X-RAY DIFFRACTION	100
2.7749-2.85	0.2234	155	0.1862	2942	X-RAY DIFFRACTION	100
2.85-2.9338	0.1932	155	0.1886	2930	X-RAY DIFFRACTION	100
2.9338-3.0285	0.2517	156	0.1962	2964	X-RAY DIFFRACTION	100
3.0285-3.1367	0.2623	156	0.1989	2975	X-RAY DIFFRACTION	100
3.1367-3.2623	0.2134	155	0.1931	2933	X-RAY DIFFRACTION	100
3.2623-3.4107	0.2249	158	0.1886	3002	X-RAY DIFFRACTION	100
3.4107-3.5905	0.2018	156	0.1839	2964	X-RAY DIFFRACTION	100
3.5905-3.8154	0.2148	157	0.1636	2987	X-RAY DIFFRACTION	100
3.8154-4.1098	0.1673	159	0.1436	3017	X-RAY DIFFRACTION	100
4.1098-4.5232	0.1434	159	0.1282	3024	X-RAY DIFFRACTION	100
4.5232-5.1771	0.152	161	0.1209	3052	X-RAY DIFFRACTION	100
5.1771-6.5203	0.1732	164	0.1694	3135	X-RAY DIFFRACTION	100
6.5203-49.7845	0.1588	175	0.1596	3322	X-RAY DIFFRACTION	100

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	1.1347	0.2183	-0.0114	2.1628	-0.4703	3.7362	-0.092	0.1606	-0.0639	-0.2603	0.0385	-0.0977	0.0652	0.1275	0.0504	0.264	0.0086	0.0355	0.2094	0.0036	0.3073	44.4564	24.1553	206.4969
2	1.2789	0.0813	0.3496	1.465	-0.2234	1.4034	-0.0428	-0.0751	0.3568	0.0183	0.0065	0.0574	-0.6878	0.0789	0.0356	0.5751	-0.0023	0.0239	0.2241	-0.0128	0.3503	50.9643	55.9219	225.5047
3	1.7122	-0.2121	-1.0587	1.0729	-0.0211	2.4659	0.1266	0.1889	-0.0802	0.0051	-0.096	0.173	-0.3403	-0.6815	-0.0289	0.2666	0.1364	-0.0328	0.4936	0.0042	0.3473	12.2375	35.2122	234.4035
4	1.9092	0.2135	0.2004	2.443	-0.2182	1.5277	-0.1524	0.8189	0.207	-0.2735	0.3826	0.1209	-0.3589	-0.5822	-0.1522	0.4853	0.2183	0.0004	1.0055	0.1184	0.3966	17.4843	46.7334	198.8874

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and resid 2:301	A	2 - 301
2	X-RAY DIFFRACTION	2	chain B and resid 3:301	B	3 - 301
3	X-RAY DIFFRACTION	3	chain C and resid 2:301	C	2 - 301
4	X-RAY DIFFRACTION	4	chain D and resid 2:301	D	2 - 301

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