PDB-3tva: Crystal Structure of Xylose isomerase domain protein from Plancto...

ID or keywords:

Entry

Database: PDB / ID: 3tva

Title

Crystal Structure of Xylose isomerase domain protein from Planctomyces limnophilus

Components

Xylose isomerase domain protein TIM barrel

Keywords

ISOMERASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG /

TIM barrel

Function / homology

Function and homology information

isomerase activity /

metal ion binding
Similarity search - Function

Biological species

Planctomyces limnophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.148 Å

Authors

Kim, Y. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of Xylose isomerase domain protein from Planctomyces limnophilus
Authors: Kim, Y. / Wu, R. / Bearden, J. / Joachimiak, A.

History

Deposition	Sep 19, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2011	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tva.cif.gz	246.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3tva.ent.gz	210 KB	Display	PDB format
PDBx/mmJSON format	3tva.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/tv/3tva ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tva	HTTPS FTP

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Related structure data

Similar structure data	6t8v-2 2htb-1 2htb-4 3rqq-d 1ekk-2 6dc1-7 3p6l-d 3pf3-d 1y7w-2 2yck-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	TargetDB: APC100605

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: Xylose isomerase domain protein TIM barrel

B: Xylose isomerase domain protein TIM barrel

hetero molecules

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

1

A: Xylose isomerase domain protein TIM barrel

hetero molecules

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

2

B: Xylose isomerase domain protein TIM barrel

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.324, 105.324, 178.936
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Details

Two monomers in the asymmetric unit

#1: Protein	Xylose isomerase domain protein TIM barrel Mass: 31912.424 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_1682 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: D5SXE5
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.89 Å³/Da / Density % sol: 68.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Magnesium Chloride, 0.1 M Sodium Cacodylate:HCl pH 6.5, 10% (w/v) PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2011 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. all: 55639 / Num. obs: 55639 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / B_iso Wilson estimate: 24.95 Å² / R_sym value: 0.092 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 10 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2727 / R_sym value: 0.736 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
RESOLVE		model building
SOLVE		phasing
PHENIX	(phenix.refine: dev_851)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.148→45.551 Å / SU ML: 0.45 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.04 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.193	2771	5.08 %	random
R_work	0.168	-	-	-
all	0.169	54539	-	-
obs	0.169	54539	98.07 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.681 Å² / k_sol: 0.335 e/Å³

Displacement parameters

B_iso mean: 30 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9512 Å²	0 Å²	-0 Å²
2-	-	0.9512 Å²	0 Å²
3-	-	-	-1.9023 Å²

Refinement step

Cycle: LAST / Resolution: 2.148→45.551 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4302	0	27	382	4711

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4818
X-RAY DIFFRACTION	f_angle_d	1.251	6603
X-RAY DIFFRACTION	f_dihedral_angle_d	13.729	1775
X-RAY DIFFRACTION	f_chiral_restr	0.096	716
X-RAY DIFFRACTION	f_plane_restr	0.007	888

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.1482-2.1852	0.2521	119	0.1937	2135	2254	83
2.1852-2.2249	0.2721	122	0.1848	2328	2460	90
2.2249-2.2677	0.2238	106	0.1766	2455	2561	94
2.2677-2.314	0.2013	122	0.1766	2545	2667	98
2.314-2.3643	0.2189	148	0.1716	2583	2731	99
2.3643-2.4193	0.2121	168	0.1738	2544	2712	100
2.4193-2.4798	0.2037	142	0.1676	2590	2732	100
2.4798-2.5469	0.2007	130	0.1679	2605	2735	100
2.5469-2.6218	0.2103	129	0.171	2636	2765	100
2.6218-2.7064	0.2462	141	0.1752	2615	2756	100
2.7064-2.8031	0.2063	147	0.1811	2599	2746	100
2.8031-2.9154	0.1987	152	0.177	2623	2775	100
2.9154-3.048	0.2051	140	0.1721	2611	2751	100
3.048-3.2087	0.2097	121	0.1656	2648	2769	100
3.2087-3.4096	0.202	144	0.175	2654	2798	100
3.4096-3.6728	0.1855	146	0.1593	2637	2783	100
3.6728-4.0422	0.1626	144	0.1458	2681	2825	100
4.0422-4.6266	0.1495	154	0.1395	2672	2826	100
4.6266-5.8271	0.163	156	0.1523	2720	2876	100
5.8271-45.5608	0.1921	140	0.2023	2887	3027	99

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	2.4287	0.4046	-0.1813	3.597	-0.837	2.0919	0.2304	0.5874	0.3909	-0.588	-0.1397	-0.1493	-0.5493	-0.188	-0.1081	0.2411	0.0529	0.0874	0.2166	0.0957	0.2741	14.4699	60.9921	-28.3352
2	6.6742	-1.2058	-2.0449	7.8079	5.1236	6.8336	0.0977	0.2124	0.3626	-0.2117	0.0476	-0.3149	-0.2026	0.2601	-0.1286	0.2028	-0.0312	0.0586	0.15	0.087	0.1482	29.3833	59.6498	-31.0547
3	1.2777	0.7608	0.0481	2.7296	1.337	2.1037	0.0788	0.1385	-0.0365	-0.1125	-0.029	-0.0258	0.021	-0.0016	-0.0505	0.1089	0.0453	0.0283	0.1385	0.0632	0.1224	21.1103	42.5649	-31.6939
4	3.0765	0.8701	-0.0172	1.9366	-0.114	1.8262	0.0822	0.1856	-0.0727	-0.2681	-0.1311	-0.0098	0.3758	0.0568	0.0382	0.145	0.0768	0.025	0.1217	0.021	0.0787	20.9189	35.7532	-21.515
5	2.0104	-0.5838	0.1842	1.1148	-0.0162	2.7449	0.0157	0.2313	0.0528	-0.2043	-0.0768	0.2002	0.075	-0.4911	0.0308	0.1046	0.0424	0.0178	0.2702	0.0547	0.1506	3.4096	43.2674	-26.6729
6	2.2697	-0.0246	-0.2109	2.1221	-1.2546	3.2685	0.1474	0.2275	0.3077	-0.2409	0.0354	0.0485	-0.1258	-0.1287	-0.1533	0.1832	0.0885	0.0734	0.2092	0.067	0.2289	3.5545	57.0585	-23.572
7	5.0845	-0.4441	-0.7555	3.0886	0.65	2.8812	-0.0278	-0.7699	0.9714	0.0153	0.1127	-0.5654	-0.6126	0.4804	-0.252	0.2251	-0.0272	0.0047	0.1358	-0.0989	0.3153	34.5389	53.7396	4.1485
8	1.3295	0.1197	-0.121	3.6234	-0.9821	2.6439	-0.0514	-0.4005	0.8197	0.5468	0.0687	-0.3143	-0.7109	-0.1721	-0.2506	0.4137	0.0457	0.0713	0.2653	-0.2262	0.4692	22.5489	62.0799	9.0485
9	1.6971	0.2308	-0.7764	2.0005	-0.5365	0.9892	0.0372	-0.5036	0.1797	0.2162	-0.0442	-0.0114	-0.1655	-0.0026	-0.0088	0.1237	0.0264	0.0233	0.2743	-0.0578	0.1427	15.8504	47.4688	10.7749
10	2.9378	0.6761	-0.897	4.2048	-2.4619	3.9868	-0.087	-0.2765	-0.2729	-0.3081	-0.1038	-0.1059	0.2757	-0.2762	0.1638	0.1362	-0.0005	0.0616	0.2209	-0.0153	0.1327	14.3645	39.9376	5.1315
11	1.3074	-0.166	0.3781	0.6775	-0.3016	1.6088	0.0762	-0.2549	-0.0792	0.0697	0.0616	-0.0245	0.1296	-0.2949	-0.0407	0.0454	0.0146	0.0377	0.1826	0.0402	0.0778	19.58	36.1771	2.2212
12	4.2651	-0.236	-0.3519	4.3087	-0.0724	5.497	-0.0425	-0.2688	-0.0899	0.3964	0.0284	-0.2007	0.205	0.1677	-0.0526	0.049	0.0353	0.009	0.1237	0.0305	0.1353	34.7788	40.3671	-1.2584
13	6.0164	0.4251	-1.0421	5.3078	0.9396	5.4753	0.1999	0.0063	0.3078	0.2202	0.0282	-0.5791	-0.158	0.8044	0.0239	0.0536	-0.0338	0.0192	0.2591	-0.0211	0.3759	43.2797	43.2982	-1.3992

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 6:38)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 39:59)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 60:128)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 129:175)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 176:236)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 237:287)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 4:37)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 38:59)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 60:111)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 112:128)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 129:236)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 237:268)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 269:287)

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