PDB-4nas: The crystal structure of a rubisco-like protein (MtnW) from Alicy...

ID or keywords:

Entry

Database: PDB / ID: 4nas

Title

The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

Components

Ribulose-bisphosphate carboxylase

RuBisCO

Keywords

LYASE /

structural genomics / PSI-Biology /

protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity /

ribulose-bisphosphate carboxylase /

carbon fixation /

ribulose-bisphosphate carboxylase activity / L-methionine salvage from methylthioadenosine / magnesium ion binding
Similarity search - Function

Biological species

Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.92 Å

Authors

Tan, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of a rubisco-like protein (MtnW) from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446.
Authors: Tan, K. / Li, H. / Clancy, S. / Joachimiak, A.

History

Deposition	Oct 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nas.cif.gz	603.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4nas.ent.gz	519.1 KB	Display	PDB format
PDBx/mmJSON format	4nas.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/na/4nas ftp://data.pdbj.org/pub/pdb/validation_reports/na/4nas	HTTPS FTP

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Related structure data

Similar structure data	2d69-2 3r9p-d 6fwf-d 4lf2-4 1tel-d 2vzt-2 2cxe-4 6ezl-d 5g4i-d 2oel-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
Other databases	TargetTrack: MCSG-APC110051

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#11 - Nov 2000 Rubisco similarity (6)

Deposited unit

A: Ribulose-bisphosphate carboxylase

B: Ribulose-bisphosphate carboxylase

C: Ribulose-bisphosphate carboxylase

D: Ribulose-bisphosphate carboxylase

hetero molecules

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

1

A: Ribulose-bisphosphate carboxylase

B: Ribulose-bisphosphate carboxylase

hetero molecules

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

2

C: Ribulose-bisphosphate carboxylase

D: Ribulose-bisphosphate carboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.763, 175.671, 83.653
Angle α, β, γ (deg.)	90.00, 107.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED THAT THE CHAINS A AND B, C AND D FORM A DIMER RESPECTIVELY.

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Ribulose-bisphosphate carboxylase / RuBisCO Mass: 44384.340 Da / Num. of mol.: 4 / Fragment: UNP residues 3-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria) Strain: DSM 446 / Gene: Aaci_0096 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)magic References: UniProt: C8WQ56, ribulose-bisphosphate carboxylase

#1: Protein

Ribulose-bisphosphate carboxylase /

RuBisCO

Mass: 44384.340 Da / Num. of mol.: 4 / Fragment: UNP residues 3-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_0096 / Plasmid: pMCSG68 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE)magic
References: UniProt: C8WQ56,

ribulose-bisphosphate carboxylase

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Non-polymers , 5 types, 648 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.24 Å³/Da / Density % sol: 45.05 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M CalCl2, 20%(w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97941 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2013 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97941 Å / Relative weight: 1
Reflection	Resolution: 1.92→29.5 Å / Num. all: 113403 / Num. obs: 113403 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.6 % / R_merge(I) obs: 0.085 / Net I/σ(I): 22.8
Reflection shell	Resolution: 1.92→1.95 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.625 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5569 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
ARP		model building
WARP		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.92→29.5 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2508	5685	5.02 %	random
R_work	0.1946	-	-	-
obs	0.1975	113354	95.66 %	-
all	-	113354	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.92→29.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11728	0	23	636	12387

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	12015
X-RAY DIFFRACTION	f_angle_d	1.071	16348
X-RAY DIFFRACTION	f_dihedral_angle_d	13.447	4309
X-RAY DIFFRACTION	f_chiral_restr	0.07	1847
X-RAY DIFFRACTION	f_plane_restr	0.006	2171

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 (%)
1.9203-1.9421	0.3996	153	0.3117	2851	X-RAY DIFFRACTION	75
1.9421-1.965	0.3418	177	0.2925	3549	X-RAY DIFFRACTION	95
1.965-1.9889	0.3789	201	0.281	3531	X-RAY DIFFRACTION	95
1.9889-2.0141	0.3378	187	0.2636	3631	X-RAY DIFFRACTION	97
2.0141-2.0406	0.3665	186	0.2672	3608	X-RAY DIFFRACTION	96
2.0406-2.0685	0.3135	176	0.2604	3592	X-RAY DIFFRACTION	97
2.0685-2.0981	0.3295	215	0.2488	3644	X-RAY DIFFRACTION	96
2.0981-2.1294	0.3134	179	0.2374	3558	X-RAY DIFFRACTION	96
2.1294-2.1626	0.3034	193	0.2379	3612	X-RAY DIFFRACTION	96
2.1626-2.1981	0.2872	176	0.2275	3614	X-RAY DIFFRACTION	95
2.1981-2.236	0.3034	173	0.2194	3557	X-RAY DIFFRACTION	96
2.236-2.2766	0.2816	179	0.2119	3604	X-RAY DIFFRACTION	96
2.2766-2.3204	0.295	204	0.2207	3527	X-RAY DIFFRACTION	95
2.3204-2.3677	0.2722	205	0.2122	3570	X-RAY DIFFRACTION	95
2.3677-2.4192	0.2877	183	0.2111	3503	X-RAY DIFFRACTION	95
2.4192-2.4754	0.2911	169	0.2178	3621	X-RAY DIFFRACTION	94
2.4754-2.5373	0.2735	192	0.2128	3502	X-RAY DIFFRACTION	94
2.5373-2.6059	0.2815	212	0.2083	3520	X-RAY DIFFRACTION	94
2.6059-2.6825	0.282	195	0.2021	3538	X-RAY DIFFRACTION	95
2.6825-2.769	0.2556	179	0.2104	3513	X-RAY DIFFRACTION	95
2.769-2.8679	0.291	215	0.2077	3580	X-RAY DIFFRACTION	95
2.8679-2.9826	0.2824	208	0.2012	3644	X-RAY DIFFRACTION	97
2.9826-3.1183	0.2612	185	0.2051	3677	X-RAY DIFFRACTION	98
3.1183-3.2825	0.2651	206	0.1969	3685	X-RAY DIFFRACTION	99
3.2825-3.4878	0.2419	198	0.1823	3741	X-RAY DIFFRACTION	99
3.4878-3.7566	0.1914	171	0.167	3753	X-RAY DIFFRACTION	99
3.7566-4.1337	0.2	194	0.1599	3741	X-RAY DIFFRACTION	100
4.1337-4.7298	0.1765	206	0.143	3793	X-RAY DIFFRACTION	100
4.7298-5.951	0.2131	187	0.1658	3749	X-RAY DIFFRACTION	100
5.951-29.5162	0.2064	181	0.1778	3661	X-RAY DIFFRACTION	95

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	2.26	-0.6301	-0.1163	2.5188	-1.2464	2.9648	0.0397	0.3776	0.0897	-0.3202	-0.1281	-0.2829	0.192	0.4657	0.0863	0.1281	0.002	-0.0296	0.3488	0.0069	0.1946	49.778	-4.9177	-2.2357
2	1.4513	-0.3206	-0.3298	0.8909	0.2001	2.379	0.018	-0.1604	0.1211	0.125	-0.0345	-0.0003	-0.3961	-0.2035	0.0019	0.2178	0.0187	-0.0651	0.19	-0.0201	0.1746	28.5605	4.3425	21.333
3	3.0551	1.3457	-1.4074	2.5389	-1.439	3.9876	-0.1525	-0.1699	-0.0895	-0.0336	-0.1128	-0.3206	-0.111	0.5198	0.2357	0.1351	-0.0289	-0.0765	0.2672	-0.0013	0.191	42.5729	0.1576	23.815
4	1.7643	0.6254	1.2692	1.2903	-0.1623	3.3481	-0.0222	-0.5721	-0.1076	0.195	-0.1582	-0.0467	-0.1963	-0.0041	0.1759	0.2496	0.0278	-0.0438	0.3641	0.0278	0.1716	33.4204	-3.4556	43.7714
5	4.2019	-2.1155	0.0491	4.0293	0.4802	3.8923	-0.1717	-0.6058	-0.5235	0.5089	0.0913	-0.0368	0.6135	-0.1221	0.021	0.2804	-0.0602	-0.0741	0.2931	0.1017	0.2734	21.8486	-21.4387	19.8306
6	1.251	0.3498	-0.1554	2.7566	0.2234	2.0025	-0.0115	-0.4462	-0.0987	0.2985	0.0916	0.1699	0.173	-0.3697	-0.0516	0.1862	-0.0504	-0.042	0.3909	0.038	0.2019	16.3093	-15.1227	19.7582
7	1.8581	-0.5789	0.971	0.9226	-0.58	2.442	0.0373	-0.0336	-0.0393	0.0102	0.0491	0.1286	0.0339	-0.3617	-0.1143	0.1292	0.0092	-0.0536	0.2254	-0.0261	0.1964	18.0609	-8.6024	1.986
8	0.8414	0.1383	-0.3393	1.9163	-0.0638	0.9941	-0.1735	0.6706	0.4212	-0.3658	-0.1102	-0.1792	-0.3209	0.3351	0.2354	0.2599	-0.0039	-0.0192	0.4357	0.1759	0.2669	34.6064	2.5376	-18.6111
9	3.04	1.9877	4.4635	3.3787	3.699	8.4083	-0.2753	0.6268	0.318	-0.8093	0.0739	-0.1597	-0.8263	0.0812	0.2182	0.4335	-0.0598	-0.0907	0.4435	0.198	0.3422	30.6728	9.9718	-24.3339
10	0.6323	0.1529	0.0305	3.0816	3.6019	8.2597	-0.0582	0.1594	0.3116	-0.2007	-0.2093	0.2354	-0.7216	-0.0848	0.2714	0.2024	-0.0051	-0.0439	0.2649	0.086	0.2415	26.2647	9.6306	-10.0278
11	0.6808	0.639	0.1782	0.8809	0.0406	1.7746	0.0159	0.1118	0.0877	-0.0517	-0.0475	0.0591	-0.0702	-0.1526	0.0469	0.1014	0.0164	-0.0513	0.2187	0.0159	0.1625	25.9863	-5.7407	-3.2141
12	2.0842	-0.7798	-0.4388	1.451	-0.1705	1.9016	-0.0308	0.1853	-0.0652	0.0422	-0.0457	0.0153	0.2338	-0.2342	0.0291	0.1248	-0.0461	-0.0444	0.2955	-0.0214	0.1606	21.3518	-14.6506	-8.572
13	3.4019	0.7429	-0.2534	2.0962	-0.5564	3.1128	-0.1103	0.6363	-0.2967	-0.3963	-0.0882	-0.1403	0.4339	0.0481	0.2274	0.3086	0.0375	-0.006	0.4288	-0.0141	0.2046	31.6344	-14.7886	-27.8787
14	1.6435	-0.914	0.0054	1.1367	-0.6399	1.3986	-0.1831	0.5968	0.2564	-0.8468	0.4567	0.0277	-0.4007	0.1273	-0.2007	0.6513	-0.172	0.0216	0.3545	0.0709	0.3579	57.9426	52.9692	-30.7363
15	2.2869	0.7295	0.0631	1.9013	-0.0016	1.1821	-0.0453	0.076	0.34	0.0537	0.1862	0.4743	-0.0672	-0.3219	-0.1311	0.342	0.0147	0.0557	0.1804	0.0047	0.4224	45.6872	42.4649	-9.4789
16	1.3826	0.0783	-0.1869	1.1532	-0.6438	1.7526	0.0058	-0.1356	-0.0192	0.5191	0.1143	0.4788	-0.1438	-0.2223	-0.0833	0.3885	0.0199	0.1275	0.1856	0.0217	0.4004	48.0424	34.5508	-1.4508
17	1.9627	0.8687	1.5766	1.3329	0.8784	5.2163	-0.1816	-0.1446	0.6255	0.1459	-0.0469	0.2446	-0.5706	-0.5251	0.1909	0.4855	0.1006	0.1461	0.264	0.0588	0.5639	43.4173	50.4865	-7.0545
18	3.8848	-0.3994	0.4573	2.4666	0.9716	4.0654	-0.4483	-0.766	0.1183	0.5588	0.1232	0.0841	-0.4823	-0.1571	0.2876	0.5766	0.1149	0.0317	0.4711	-0.0652	0.398	39.3424	50.373	14.2905
19	3.8432	-0.741	-0.8118	1.2063	0.4697	2.3788	0.09	-0.5998	-0.0376	0.712	-0.2454	-0.2652	-0.363	0.1724	0.1119	0.5168	-0.1243	-0.1314	0.3987	0.0149	0.2991	70.6194	44.6541	5.3292
20	3.138	0.879	-1.0148	2.0678	-0.4796	1.7912	0.3434	-0.8108	-0.3074	0.7048	-0.3347	-0.4019	0.204	0.134	0.0179	0.674	-0.1308	-0.152	0.5553	0.0554	0.3336	70.2318	40.483	9.3991
21	4.275	1.5102	0.288	2.5463	0.4255	2.5892	0.3062	-0.5813	-0.2817	0.6352	-0.4417	-0.3769	0.143	0.2265	0.1187	0.3943	-0.0243	-0.0668	0.2571	0.0753	0.3291	67.5459	36.6747	-0.1324
22	0.5877	-0.3896	-0.9404	1.7442	1.0708	2.3952	-0.2435	-0.1225	-0.5139	-0.0686	-0.0653	-0.4904	0.1003	0.4528	0.2134	0.3727	-0.0143	0.1614	0.2991	0.0179	0.7567	71.2032	30.8497	-11.4671
23	1.1446	0.5167	-0.1551	1.3888	0.4768	0.9221	-0.4213	0.2951	-0.1615	-1.0245	0.3258	-0.2997	0.0505	0.0901	0.099	1.0547	-0.3112	0.1999	0.3817	-0.1769	0.4386	65.6488	32.8455	-39.029
24	0.7102	-0.187	-0.2164	0.7976	0.5191	1.4637	-0.3143	0.1669	-0.3356	-0.7855	0.2356	-0.3189	0.1859	0.0786	0.0329	0.5593	-0.11	0.1615	0.2372	-0.1111	0.447	65.3301	30.5647	-25.9099
25	0.793	-0.6144	0.7358	1.4955	0.5294	1.8857	-0.3019	-0.1005	-0.2846	-0.3136	0.1433	-0.6979	-0.1001	0.542	-0.0107	0.3665	-0.0101	0.2735	0.3723	-0.0439	0.8467	79.403	34.253	-19.6491
26	0.6844	-0.2955	0.5586	0.1214	-0.2367	0.485	-0.2796	0.5604	0.0534	-0.3703	-0.0568	-0.3294	0.0272	0.4497	-0.0443	1.0428	-0.4124	0.8399	0.6609	-0.0989	0.9606	84.5101	37.4858	-39.7422

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 98 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 311 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 312 through 340 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 341 through 408 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 35 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 36 through 98 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 99 through 136 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 137 through 187 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 188 through 206 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 207 through 232 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 233 through 311 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 312 through 340 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 341 through 408 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 10 through 98 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 99 through 155 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 156 through 311 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 312 through 340 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 341 through 408 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 9 through 35 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 36 through 71 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 72 through 98 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 99 through 136 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 137 through 187 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 188 through 311 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 312 through 340 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 341 through 407 )

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