PDB-3t4c: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase fr...

ID or keywords:

Entry

Database: PDB / ID: 3t4c

Title

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia ambifaria

Components

2-dehydro-3-deoxyphosphooctonate aldolase 1

Keywords

TRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

molecular replacement / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...

History

Deposition	Jul 25, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 17, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Sep 13, 2023	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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3t4c.cif.gz	409.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3t4c.ent.gz	339.2 KB	Display	PDB format
PDBx/mmJSON format	3t4c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3t4c_validation.pdf.gz	450 KB	Display	wwPDB validaton report
Full document	3t4c_full_validation.pdf.gz	457 KB	Display
Data in XML	3t4c_validation.xml.gz	42.4 KB	Display
Data in CIF	3t4c_validation.cif.gz	61.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4c ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4c	HTTPS FTP

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Related structure data

Related structure data	3d63C 3dahC 3eizC 3ej2C 3ek2C 3ezoC 3f0fC 3ftpC 3gk0C 3gk3C 3gvfC 3gwaC 3gweC 3imlC 3sz8SC 3tmlC 3tmqC 3txyC 3u7jC 3ue9C 3uk1C 3uk2C 3undC 3uptC 3urrC 3uw1C 3uw2C 3uw3C 3v2iC 3v7nC 3v8hC 3v9oC 3v9pC 3vavC 4ddoC 4dfeC 4dheC 4dhkC 4dutC 4dz4C 4e4tC 4efiC 4eg0C 4egjC 4ek2C 4eqyC 4ewgC 4exqC 4f2gC 4f32C 4f3nC 4f3yC 4f4hC 4f7dC 4fk8C 4fryC 4g1kC 4g67C 4ghkC 4h3yC 4h3zC 4h4gC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tmq-d 3sz8-d 1o60-d 1gg0-1 3fyp-d 1pl9-1 1phq-1 1d9e-d 6bng-1 1x8f-1 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: BuamA.00102.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 2-dehydro-3-deoxyphosphooctonate aldolase 1

B: 2-dehydro-3-deoxyphosphooctonate aldolase 1

C: 2-dehydro-3-deoxyphosphooctonate aldolase 1

D: 2-dehydro-3-deoxyphosphooctonate aldolase 1

125 kDa, 4 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)	49.130, 129.500, 169.390
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	2-dehydro-3-deoxyphosphooctonate aldolase 1 / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 1 / KDO-8-phosphate synthase 1 / Phospho-2- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 1 / KDO-8-phosphate synthase 1 / Phospho-2-dehydro-3-deoxyoctonate aldolase 1 Mass: 31265.650 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: kdsA1, BamMC406_2018 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B1YT10, 3-deoxy-8-phosphooctulonate synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

2-dehydro-3-deoxyphosphooctonate aldolase 1 / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase 1 / KDO-8-phosphate synthase 1 / Phospho-2- ...

Mass: 31265.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: kdsA1, BamMC406_2018 / Plasmid: AVA0421 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1YT10, 3-deoxy-8-phosphooctulonate synthase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.32 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: EBS internal tracking number 224045c2 WIZARD 3/4 C2. 24%(w/v) PEG 1500, 20%(v/v) Glycerol, BuamA.00102.a.A1 PS01117 at 74 mg/mL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 12, 2011

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.95→45.94 Å / Num. obs: 79104 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / B_iso Wilson estimate: 30.992 Å² / R_merge(I) obs: 0.087 / Net I/σ(I): 12.71

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.95-2		2.8	0.401	2.4	14575	5228	89.8
2-2.06			0.34	3.2	18819	5614	98.1
2.06-2.12			0.282	4.7	23720	5501	99.7
2.12-2.18			0.267	6.4	31883	5379	100
2.18-2.25			0.243	7.7	36184	5214	100
2.25-2.33			0.219	8.4	35274	5063	100
2.33-2.42			0.182	9.8	33829	4852	99.9
2.42-2.52			0.165	10.8	32844	4700	99.9
2.52-2.63			0.141	12.1	31204	4494	99.7
2.63-2.76			0.13	13.2	30399	4359	99.8
2.76-2.91			0.107	15.4	28300	4096	99.7
2.91-3.08			0.096	17.1	26712	3929	99.8
3.08-3.3			0.085	19	24641	3654	99.7
3.3-3.56			0.073	22.2	22743	3437	99.6
3.56-3.9			0.066	23.5	20384	3129	99.6
3.9-4.36			0.059	25.4	19015	2908	99.6
4.36-5.03			0.058	26.1	16776	2566	99.7
5.03-6.17			0.054	25.6	14975	2220	99.8
6.17-8.72			0.045	26.2	11727	1734	99.8
	8.72		0.036	27.2	6407	1027	97.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	45.94 Å
Translation	2.5 Å	45.94 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
XDS		data reduction

Refinement

Method to determine structure:

molecular replacement
Starting model: 3SZ8

3sz8

Resolution: 1.95→44.33 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.948 / SU B: 6.168 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.203	3951	5 %	RANDOM
R_work	0.17	-	-	-
obs	0.172	78773	98.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 28.114 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.5 Å²	0 Å²	0 Å²
2-	-	0.43 Å²	0 Å²
3-	-	-	-0.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→44.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7890	0	0	561	8451

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	8164
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5437
X-RAY DIFFRACTION	r_angle_refined_deg	1.494	1.969	11102
X-RAY DIFFRACTION	r_angle_other_deg	0.969	3	13327
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.475	5	1077
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.003	24.345	359
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.701	15	1347
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.176	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	1293
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	9209
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1593

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	246	-
R_work	0.246	4751	-
all	-	4997	-
obs	-	-	89.28 %

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	2.2583	-1.0263	0.2436	1.2969	-0.6682	3.1607	-0.0702	-0.1731	-0.0677	0.2774	-0.046	-0.0156	-0.0681	0.2649	0.1162	0.151	-0.0499	-0.0239	0.186	0.0038	0.0144	46.141	133.798	97.818
2	0.5072	-0.0305	0.27	0.641	-0.1734	2.1102	-0.0028	-0.1023	-0.0095	0.0744	0.0709	0.0651	0.0324	-0.2075	-0.0681	0.091	-0.0171	0.011	0.1601	0.0173	0.0637	30.415	130.486	85.975
3	1.6303	-0.156	0.5252	0.7776	-1.281	2.5642	0.019	0.0356	-0.0446	0.0655	-0.1128	-0.073	-0.2034	0.3803	0.0938	0.1234	-0.0685	-0.0345	0.152	0.0031	0.0628	47.428	140.357	82.68
4	1.7219	-0.4587	-0.563	0.7412	-0.4018	2.7999	-0.006	0.0766	0.0329	-0.1374	-0.0593	-0.0118	0.0792	0.3994	0.0653	0.1684	0.0067	-0.0039	0.1822	0.0222	0.0037	38.933	122.624	30.469
5	0.4022	0.0549	0.3924	0.2471	0.2573	2.0034	0.0161	0.029	0.069	-0.0813	-0.0222	0.035	-0.3328	0.0763	0.0061	0.1862	0.0046	-0.011	0.11	0.0319	0.0685	29.724	133.571	43.659
6	1.3669	-0.4527	-0.0801	0.4438	-0.0488	1.8313	0.0245	-0.0111	-0.0478	-0.0666	-0.0484	-0.0015	0.2736	0.3099	0.0239	0.165	0.0502	-0.0004	0.1433	0.0104	0.0311	36.075	114.488	45.586
7	2.6719	0.3607	-1.5536	0.701	-1.406	3.1117	0.0277	-0.0835	-0.0372	-0.123	0.2086	0.1232	0.2295	-0.3323	-0.2363	0.1347	-0.0572	-0.0606	0.1198	0.0599	0.136	14.566	101.637	69.005
8	0.2805	0.0995	0.0541	1.3371	-0.6725	0.8802	0.0283	-0.0978	-0.0264	0.0497	-0.0412	0.0083	-0.0077	0.0699	0.0129	0.0995	-0.0086	-0.0027	0.1421	0.0356	0.0786	31.656	109.712	73.862
9	1.4682	0.0666	0.0277	0.9959	-0.896	1.4796	0.0529	-0.0093	0.0631	-0.094	0.0926	0.1826	0.1113	-0.1794	-0.1455	0.1087	-0.0308	-0.0276	0.113	0.0312	0.0981	19.429	112.707	58.029
10	0.572	-1.2238	-0.1337	4.4216	-1.6829	2.1922	0.1559	0.087	-0.0014	-0.179	-0.2569	-0.0755	-0.2536	0.0806	0.101	0.1966	-0.089	-0.0222	0.141	0.032	0.1028	42.453	161.501	55.776
11	0.1868	0.0471	0.2426	1.7326	-0.1257	1.047	0.0378	0.029	0.0412	-0.1948	-0.0908	-0.1998	-0.0307	0.2334	0.0531	0.1117	-0.0352	0.0392	0.1791	0.031	0.091	48.614	144.907	56.855
12	0.9233	-0.3881	-0.0804	2.784	-1.5454	1.9734	0.0048	0.0515	0.0978	0.229	0.0588	0.2363	-0.3587	-0.0379	-0.0636	0.1587	-0.0339	0.0041	0.066	0.0092	0.0941	37.386	153.9	70.659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 88
2	X-RAY DIFFRACTION	2	A	89 - 200
3	X-RAY DIFFRACTION	3	A	201 - 281
4	X-RAY DIFFRACTION	4	B	1 - 103
5	X-RAY DIFFRACTION	5	B	104 - 198
6	X-RAY DIFFRACTION	6	B	199 - 281
7	X-RAY DIFFRACTION	7	C	1 - 83
8	X-RAY DIFFRACTION	8	C	84 - 198
9	X-RAY DIFFRACTION	9	C	199 - 281
10	X-RAY DIFFRACTION	10	D	1 - 116
11	X-RAY DIFFRACTION	11	D	117 - 198
12	X-RAY DIFFRACTION	12	D	199 - 281

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