PDB-3r1x: Crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsie...

ID or keywords:

Entry

Database: PDB / ID: 3r1x

Title

Crystal structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae

Components

2-oxo-3-deoxygalactonate kinase

Keywords

TRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / 2-oxo-3-deoxygalactonate kinase / 2-dehydro-3-deoxygalactonokinase / 2-keto-3-deoxygalactonate kinase / DeLey-Doudoroff pathway

Function / homology

Function and homology information

2-dehydro-3-deoxygalactonokinase activity / D-galactonate catabolic process
Similarity search - Function

Biological species

Klebsiella pneumoniae subsp. pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.093 Å

Authors

Michalska, K. / Cuff, M.E. / Tesar, C. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.
Authors: Michalska, K. / Cuff, M.E. / Tesar, C. / Feldmann, B. / Joachimiak, A.

History

Deposition	Mar 11, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2011	Provider: repository / Type: Initial release
Supersession	Jun 15, 2011	ID: 3NUW
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 10, 2011	Group: Database references
Revision 1.3	Sep 21, 2011	Group: Other

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3r1x.cif.gz	478.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3r1x.ent.gz	417.1 KB	Display	PDB format
PDBx/mmJSON format	3r1x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3r1x_validation.pdf.gz	477.9 KB	Display	wwPDB validaton report
Full document	3r1x_full_validation.pdf.gz	490.9 KB	Display
Data in XML	3r1x_validation.xml.gz	49.2 KB	Display
Data in CIF	3r1x_validation.cif.gz	70.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r1/3r1x ftp://data.pdbj.org/pub/pdb/validation_reports/r1/3r1x	HTTPS FTP

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Related structure data

Similar structure data	6nmv-d 1o89-1 6bt9-2 2o1w-2 3c0b-2 4o8k-d 1gle-d 3cet-d 6txz-4 4i77-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: APC38818 TargetDB: APC106681

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 2-oxo-3-deoxygalactonate kinase

B: 2-oxo-3-deoxygalactonate kinase

C: 2-oxo-3-deoxygalactonate kinase

D: 2-oxo-3-deoxygalactonate kinase

hetero molecules

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

1

A: 2-oxo-3-deoxygalactonate kinase

B: 2-oxo-3-deoxygalactonate kinase

hetero molecules

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

2

C: 2-oxo-3-deoxygalactonate kinase

D: 2-oxo-3-deoxygalactonate kinase

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	85.509, 134.026, 139.906
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	2-oxo-3-deoxygalactonate kinase Mass: 31673.078 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: ATCC 700721 / MGH 78578 / Gene: dgoK, KPN78578_40560, KPN_04097 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, pRK1037 References: UniProt: A6TFZ6, 2-dehydro-3-deoxygalactonokinase
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 540 / 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: 3.16 Å³/Da / Density % sol: 61.12 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M magnesium formate, 15%(w/v) PEG3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792064 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 5, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792064 Å / Relative weight: 1
Reflection	Resolution: 2.093→50 Å / Num. all: 95105 / Num. obs: 94834 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / B_iso Wilson estimate: 29.9 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 14.5
Reflection shell	Resolution: 2.093→2.14 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.684 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4700 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELX		model building
MLPHARE		phasing
DM		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.093→35.2 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.95 / SU B: 8.316 / SU ML: 0.099 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19915	1902	2 %	RANDOM
R_work	0.17398	-	-	-
all	0.17448	94473	-	-
obs	0.17448	94473	99.16 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 41.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0 Å²
2-	-	-0.82 Å²	0 Å²
3-	-	-	1.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.093→35.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8795	0	114	540	9449

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	9438
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6285
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	1.954	12863
X-RAY DIFFRACTION	r_angle_other_deg	0.95	3	15255
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.124	5	1237
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.211	23.079	406
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.758	15	1448
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.848	15	86
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1451
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10804
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1958
X-RAY DIFFRACTION	r_mcbond_it	0.647	1.5	6026
X-RAY DIFFRACTION	r_mcbond_other	0.179	1.5	2479
X-RAY DIFFRACTION	r_mcangle_it	1.17	2	9638
X-RAY DIFFRACTION	r_scbond_it	2.102	3	3412
X-RAY DIFFRACTION	r_scangle_it	3.252	4.5	3221

LS refinement shell

Resolution: 2.093→2.147 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	166	-
R_work	0.234	6482	-
obs	-	6482	95.61 %

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	1.574	-0.0042	0.303	6.1754	1.9326	4.4038	0.0538	-0.064	-0.1653	0.2523	-0.0901	-0.1605	0.037	-0.0715	0.0363	0.0832	-0.0193	-0.0267	0.0966	0.029	0.1371	66.8041	121.3405	34.6966
2	1.2353	1.1526	1.1092	11.0904	3.8442	6.0511	-0.0457	-0.2028	-0.1401	0.3982	0.0934	-0.5185	0.0026	0.4069	-0.0477	0.198	-0.0482	-0.0669	0.1991	0.0366	0.2256	74.2954	128.3731	41.4875
3	3.3263	-0.149	2.4952	2.2287	-1.048	4.836	0.0516	0.1714	0.0766	-0.1897	-0.1501	-0.2609	-0.2827	0.1843	0.0985	0.0987	-0.0154	0.0652	0.0873	-0.0045	0.1112	67.6432	134.5693	24.9509
4	7.3485	-4.1933	1.046	5.7978	-0.8438	1.5604	0.0495	0.1859	0.141	-0.1356	-0.1538	-0.3469	-0.0808	0.1198	0.1043	0.111	-0.0256	0.0437	0.0751	-0.0236	0.0534	64.1478	136.5511	22.8985
5	1.4072	-0.7393	-1.0514	1.4648	0.6846	1.2832	-0.0292	-0.0586	-0.1936	0.033	-0.0311	0.241	0.0522	-0.0074	0.0603	0.1065	-0.0128	-0.0026	0.1042	-0.0133	0.1351	40.9235	136.8812	32.6631
6	8.2913	-2.5834	0.4247	3.2695	0.3937	0.7784	0.0665	0.3388	-0.1581	-0.1998	-0.1932	0.404	0.0764	-0.1201	0.1267	0.1805	-0.036	0.0068	0.1198	-0.0497	0.1411	48.8374	125.6763	24.3955
7	1.5376	-1.6714	0.9588	8.4279	-1.2086	3.8331	0.0209	-0.0195	0.0545	0.1156	-0.0645	-0.2542	-0.0923	0.1796	0.0435	0.1283	-0.0179	0.0345	0.1432	0.0394	0.0768	31.8666	173.559	57.3656
8	2.221	-3.3547	-1.3895	8.5241	2.4629	3.5673	-0.1549	-0.2827	-0.0426	0.4922	0.202	-0.3532	0.1056	0.207	-0.0471	0.2165	0.0169	0.0005	0.2408	0.0701	0.1201	33.4874	165.9889	66.5175
9	2.337	1.3136	1.9038	3.7307	3.5636	4.9986	0.0639	-0.0718	-0.397	0.2903	-0.1267	0.2392	0.4926	-0.2355	0.0628	0.1524	-0.0019	0.0848	0.1359	0.0639	0.1948	24.0498	158.2499	55.0314
10	1.1021	0.0595	-0.5248	2.7714	0.1089	2.4799	0.0445	-0.0434	-0.213	0.1456	-0.0499	0.2553	-0.0207	-0.2114	0.0054	0.0824	0.0149	0.0357	0.1291	0.0086	0.2094	21.9627	161.3661	45.9709
11	3.9294	-0.4511	-0.8828	1.3553	0.2538	0.7971	0.0644	-0.0374	0.1087	-0.0678	-0.0428	0.016	-0.1449	0.0455	-0.0216	0.1302	0.016	0.0051	0.0682	-0.0037	0.058	43.4827	155.7571	32.316
12	2.9291	-1.7295	-3.0621	2.2596	1.9953	5.7713	0.1908	0.2488	0.0827	-0.3168	-0.1795	0.108	-0.2087	-0.1988	-0.0113	0.1576	0.034	0.0012	0.0941	0.034	0.1392	30.6656	168.6147	36.6121
13	24.9001	2.9709	-1.4837	3.1312	-9.0931	28.7822	0.4871	-1.9337	-2.0653	-0.6887	0.359	0.0992	2.5057	-1.3221	-0.8461	0.8677	-0.1372	-0.0285	0.3927	0.2169	0.6641	53.3451	112.6776	60.9175
14	3.767	-1.338	0.0675	7.463	1.1083	3.902	0.1174	0.0334	-0.5161	-0.1927	-0.2624	0.4081	0.4929	-0.3936	0.145	0.2486	-0.0272	-0.0008	0.2596	0.0002	0.2737	50.625	123.7982	50.4423
15	2.9838	0.6154	0.239	2.0467	0.3008	1.5988	0.0372	-0.1864	-0.2969	0.3012	-0.0742	0.0896	0.2904	-0.2226	0.037	0.2839	-0.0232	0.0152	0.3098	0.0778	0.1252	57.8884	134.702	65.3703
16	2.1063	0.631	-1.3123	1.5268	0.1383	2.2297	-0.0906	-0.0672	-0.1717	-0.0093	0.1281	-0.3227	0.1045	0.1312	-0.0375	0.0838	0.0235	-0.0302	0.1687	-0.0234	0.1845	76.3648	146.0735	50.6053
17	2.4404	-0.4648	3.4735	0.4253	1.247	15.845	0.0455	-0.2055	0.3954	0.114	0.1861	-0.2462	0.4676	0.3139	-0.2316	0.5751	0.0055	-0.1547	0.5043	0.1117	0.3593	74.4626	136.9823	70.3787
18	9.9523	5.6363	0.1514	6.0879	-0.0592	1.055	0.2074	-0.4797	-0.2796	0.4424	-0.1394	-0.2151	0.4122	0.1441	-0.068	0.3442	0.0937	-0.0316	0.2685	0.117	0.2313	69.5475	128.4657	60.9865
19	4.2841	-0.1953	-0.1408	7.5028	0.5466	3.9374	-0.0676	0.6669	0.4217	-1.1801	0.0694	0.5785	-0.5859	-0.4505	-0.0018	0.5718	-0.0914	-0.0239	0.4603	0.0675	0.2864	71.8888	175.2068	25.3282
20	2.1276	0.3661	-0.698	4.7845	-2.4354	4.484	-0.0711	0.2604	0.176	-0.3472	-0.0073	-0.4055	-0.2114	0.3765	0.0784	0.2118	-0.1189	0.0974	0.2711	-0.0905	0.2887	85.7948	169.0156	36.9148
21	2.4579	1.697	-0.2607	3.5665	-0.1565	1.356	-0.1116	0.1626	0.2258	-0.2353	0.2693	-0.289	-0.3622	0.1308	-0.1577	0.1792	-0.0595	0.0462	0.2133	-0.0502	0.1955	77.7718	169.3828	48.0636
22	5.6817	0.2602	2.1258	3.281	0.5201	3.1878	0.0533	0.009	-0.0573	-0.0457	0.1151	0.1702	0.1548	-0.4354	-0.1684	0.1225	0.0108	0.0661	0.2912	0.0464	0.1191	58.8252	158.2737	56.236
23	5.6557	1.0951	-1.3101	3.7869	-0.5532	2.0826	0.0575	-0.0534	0.0403	0.1679	0.0881	0.1811	0.0025	-0.2741	-0.1457	0.1114	0.0261	-0.0087	0.2353	0.0039	0.0206	61.2566	155.8498	57.8035
24	1.3544	1.3978	-2.1891	2.7772	-3.0071	7.2987	-0.0086	-0.0803	0.2943	0.1445	0.0227	-0.1487	-0.624	0.2336	-0.0141	0.3138	-0.0053	0.0476	0.1992	-0.0387	0.32	73.6992	176.3461	49.1122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 36
2	X-RAY DIFFRACTION	2	A	37 - 56
3	X-RAY DIFFRACTION	3	A	57 - 87
4	X-RAY DIFFRACTION	4	A	88 - 121
5	X-RAY DIFFRACTION	5	A	122 - 238
6	X-RAY DIFFRACTION	6	A	239 - 292
7	X-RAY DIFFRACTION	7	B	1 - 32
8	X-RAY DIFFRACTION	8	B	33 - 58
9	X-RAY DIFFRACTION	9	B	59 - 82
10	X-RAY DIFFRACTION	10	B	83 - 135
11	X-RAY DIFFRACTION	11	B	136 - 238
12	X-RAY DIFFRACTION	12	B	239 - 292
13	X-RAY DIFFRACTION	13	C	1 - 5
14	X-RAY DIFFRACTION	14	C	6 - 75
15	X-RAY DIFFRACTION	15	C	76 - 148
16	X-RAY DIFFRACTION	16	C	149 - 238
17	X-RAY DIFFRACTION	17	C	239 - 249
18	X-RAY DIFFRACTION	18	C	250 - 292
19	X-RAY DIFFRACTION	19	D	1 - 75
20	X-RAY DIFFRACTION	20	D	76 - 121
21	X-RAY DIFFRACTION	21	D	122 - 168
22	X-RAY DIFFRACTION	22	D	169 - 198
23	X-RAY DIFFRACTION	23	D	199 - 239
24	X-RAY DIFFRACTION	24	D	240 - 292

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