PDB-4rit: The yellow crystal structure of pyridoxal-dependent decarboxylase...

ID or keywords:

Entry

Database: PDB / ID: 4rit

Title

The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

Components

Pyridoxal-dependent decarboxylase

Keywords

LYASE / MCSG /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / A/B/A FOLD /

DECARBOXYLASE /

CYTOSOLIC

Function / homology

Function and homology information

carboxy-lyase activity / carboxylic acid metabolic process /

pyridoxal phosphate binding
Similarity search - Function

Biological species

Sphaerobacter thermophilus DSM 20745 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
Authors: Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Oct 7, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rit.cif.gz	384.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4rit.ent.gz	326.5 KB	Display	PDB format
PDBx/mmJSON format	4rit.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ri/4rit ftp://data.pdbj.org/pub/pdb/validation_reports/ri/4rit	HTTPS FTP

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Related structure data

Similar structure data	4rj0-1 6bom-3 6bop-1 5vif-d 2x3l-d 4xmu-d 4f5f-d 5uqq-3 4rj0-2 5uqo-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC100677

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: Pyridoxal-dependent decarboxylase

A: Pyridoxal-dependent decarboxylase

hetero molecules

109 kDa, 2 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)	77.483, 118.566, 126.018
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pyridoxal-dependent decarboxylase Mass: 53772.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria) Strain: DSM 20745 / Gene: Sthe_2364 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D1C7D8, glutamate decarboxylase
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.69 Å³/Da / Density % sol: 54.29 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.8M LICL, 0.1M TRIS:HCL, 8% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011 / Details: MIRRORS
Radiation	Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97924 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 107436 / Num. obs: 103528 / % possible obs: 99.3 % / Redundancy: 5.6 % / B_iso Wilson estimate: 23.7 Å² / R_sym value: 0.083 / Net I/σ(I): 7.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.526 / Mean I/σ(I) obs: 2.27 / R_sym value: 0.526 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.8→39.595 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 15.97 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.1732	5354	4.99 %
R_work	0.1504	-	-
obs	0.1515	107329	99.21 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→39.595 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7119	0	93	558	7770

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	7627
X-RAY DIFFRACTION	f_angle_d	1.7	10393
X-RAY DIFFRACTION	f_dihedral_angle_d	14.984	2821
X-RAY DIFFRACTION	f_chiral_restr	0.086	1157
X-RAY DIFFRACTION	f_plane_restr	0.008	1372

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 (%)
1.8-1.8193	0.2694	152	0.2295	3245	X-RAY DIFFRACTION	96
1.8193-1.8407	0.2535	189	0.2146	3393	X-RAY DIFFRACTION	100
1.8407-1.8632	0.2101	169	0.1951	3354	X-RAY DIFFRACTION	99
1.8632-1.8867	0.1919	152	0.1806	3438	X-RAY DIFFRACTION	100
1.8867-1.9116	0.1978	171	0.1706	3352	X-RAY DIFFRACTION	100
1.9116-1.9378	0.1916	184	0.1671	3423	X-RAY DIFFRACTION	100
1.9378-1.9654	0.2129	162	0.1681	3347	X-RAY DIFFRACTION	100
1.9654-1.9948	0.2213	179	0.1579	3409	X-RAY DIFFRACTION	100
1.9948-2.0259	0.1716	156	0.162	3387	X-RAY DIFFRACTION	100
2.0259-2.0592	0.1852	206	0.1603	3369	X-RAY DIFFRACTION	100
2.0592-2.0947	0.2255	198	0.1562	3376	X-RAY DIFFRACTION	100
2.0947-2.1327	0.1793	173	0.1412	3387	X-RAY DIFFRACTION	100
2.1327-2.1738	0.1571	178	0.1374	3409	X-RAY DIFFRACTION	100
2.1738-2.2181	0.165	193	0.1416	3408	X-RAY DIFFRACTION	100
2.2181-2.2664	0.1707	174	0.1448	3376	X-RAY DIFFRACTION	100
2.2664-2.3191	0.1812	144	0.1485	3447	X-RAY DIFFRACTION	100
2.3191-2.3771	0.1843	171	0.1467	3407	X-RAY DIFFRACTION	100
2.3771-2.4413	0.181	179	0.1501	3432	X-RAY DIFFRACTION	100
2.4413-2.5132	0.1797	166	0.1502	3417	X-RAY DIFFRACTION	100
2.5132-2.5943	0.1733	190	0.1464	3408	X-RAY DIFFRACTION	100
2.5943-2.687	0.1858	170	0.1491	3430	X-RAY DIFFRACTION	100
2.687-2.7945	0.1696	200	0.1463	3410	X-RAY DIFFRACTION	100
2.7945-2.9217	0.1833	178	0.1587	3407	X-RAY DIFFRACTION	100
2.9217-3.0756	0.1637	213	0.1591	3426	X-RAY DIFFRACTION	100
3.0756-3.2682	0.1641	193	0.154	3422	X-RAY DIFFRACTION	100
3.2682-3.5204	0.1666	170	0.1481	3469	X-RAY DIFFRACTION	99
3.5204-3.8745	0.1458	183	0.1408	3401	X-RAY DIFFRACTION	98
3.8745-4.4344	0.1494	167	0.1294	3407	X-RAY DIFFRACTION	97
4.4344-5.5844	0.1689	193	0.1362	3402	X-RAY DIFFRACTION	97
5.5844-39.6041	0.1659	201	0.1589	3417	X-RAY DIFFRACTION	93

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	3.293	0.7032	-1.9441	1.8843	-0.6306	2.8069	0.2714	-0.2433	0.4469	0.4823	-0.0001	0.3079	-0.6183	-0.1599	-0.259	0.2948	0.0519	0.0443	0.2076	-0.0273	0.2735	3.6091	32.8272	35.0707
2	1.6581	0.1471	-1.5376	0.787	0.4654	2.9314	0.0606	-0.3383	0.1701	0.2042	-0.0108	-0.0031	-0.2219	0.4573	-0.0501	0.2796	-0.0266	-0.0033	0.2381	-0.0151	0.2388	23.0941	29.52	29.385
3	1.4928	-0.8111	-0.5855	1.668	0.4856	2.0168	-0.027	0.0972	-0.0899	-0.0046	0.011	0.3232	0.0849	-0.2731	0.0051	0.1652	-0.0062	-0.0188	0.2054	0.0252	0.2341	4.452	11.2728	18.4941
4	2.1638	0.8176	0.1071	4.2486	-1.0169	3.7445	0.0127	-0.0575	-0.334	-0.1272	-0.1025	-0.2486	0.4975	0.0407	0.0887	0.2008	0.0245	0.0076	0.1842	0.0042	0.1957	20.0221	-9.6057	21.0144
5	0.7327	0.3991	0.0206	1.338	-0.827	1.6627	-0.0325	0.0428	-0.2078	-0.166	-0.034	-0.195	0.269	0.2441	0.066	0.2067	0.0537	0.0207	0.2069	-0.0142	0.1936	28.7336	-1.8283	9.5552
6	0.7331	-0.0336	-0.4733	2.154	-0.0417	1.7901	-0.0104	0.1071	-0.0251	-0.1359	0.0403	0.1927	0.1065	-0.1762	-0.0221	0.1267	0.0098	-0.0376	0.1636	0.0019	0.1612	13.2742	5.6271	13.179
7	3.1351	0.4054	-0.82	0.8099	-0.1781	0.9871	0.0158	0.1813	0.0684	-0.0762	-0.0432	-0.1216	-0.063	0.1211	0.0242	0.1868	0.0063	-0.0017	0.1569	0.0252	0.1785	32.8672	22.0085	7.1283
8	2.8629	-0.8861	-0.4034	2.1938	-0.0962	2.2361	0.0985	0.0134	0.2273	-0.0386	-0.0794	-0.3164	-0.2119	0.3429	-0.0381	0.1579	-0.0464	0.0003	0.1985	0.0224	0.1752	37.814	27.1866	10.6983
9	1.3873	0.1723	-1.2491	0.8118	-0.4409	2.5487	0.1448	0.1201	0.3408	0.0235	0.0166	0.2462	-0.4686	-0.2366	-0.1706	0.254	0.0462	-0.0151	0.1872	0.0295	0.3033	6.8752	33.7752	17.3366
10	1.1032	0.5412	0.0778	0.927	-0.5787	0.6044	-0.1098	0.4317	-0.1703	-0.0819	-0.063	0.458	0.2939	-0.6908	-0.0445	0.1787	0.0392	-0.0298	0.3109	0.0503	0.2957	-5.3947	16.698	17.3816
11	0.9809	0.5637	-0.5465	0.316	-0.4013	1.8532	-0.0355	0.0779	0.1231	-0.0033	0.0572	0.1522	0.0009	-0.2105	-0.078	0.1928	0.0546	0.0195	0.2421	0.0317	0.3018	-3.6151	18.5858	27.5899
12	0.9455	0.0595	-0.4283	2.5551	-1.035	2.5264	-0.0225	-0.1506	0.13	0.1449	-0.059	-0.2292	-0.1527	0.2745	0.077	0.1664	-0.0098	-0.0156	0.1796	-0.0303	0.1857	21.5569	18.8291	34.7572
13	3.2182	-0.1028	-1.2136	1.298	-0.2427	2.7186	-0.0667	-0.0192	-0.2541	-0.0083	-0.028	-0.1105	0.3223	0.2115	0.0825	0.2161	0.0378	-0.0169	0.2005	0.018	0.1666	22.1306	-7.6305	34.9253
14	2.1321	-0.0353	-1.8431	1.1477	0.3136	4.3361	-0.0743	-0.2456	-0.3005	0.1643	-0.0277	-0.0016	0.39	0.1009	0.1118	0.1941	-0.0011	-0.0108	0.1575	0.0485	0.1892	12.6977	-11.7758	42.3286
15	1.228	-0.2496	-0.1333	1.2788	-0.8216	1.5631	-0.0649	-0.202	0.0334	0.1498	0.0418	-0.0809	0.0134	0.1311	0.0176	0.169	0.0197	-0.0163	0.193	-0.008	0.1377	17.9279	3.8823	42.7748
16	2.7922	1.03	-0.3058	1.9435	-0.5413	1.0973	0.0917	-0.3373	-0.0321	0.2637	0.0314	0.4592	0.027	-0.2203	-0.1149	0.219	0.0496	0.0492	0.2613	0.0565	0.2906	-6.1296	6.429	46.1314
17	1.2649	0.3782	-0.122	2.058	0.1961	1.3609	0.0279	-0.085	-0.0182	0.1812	0.1284	0.7613	0.0227	-0.373	-0.1332	0.192	0.022	0.0404	0.2997	0.0717	0.3844	-12.5948	6.7557	42.5646

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 5 through 38 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 39 through 96 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 97 through 150 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 151 through 180 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 181 through 281 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 282 through 354 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 355 through 433 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 434 through 480 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 5 through 38 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 39 through 64 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 65 through 96 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 97 through 150 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 151 through 191 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 192 through 233 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 234 through 354 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 355 through 433 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 434 through 477 )

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