PDB-3e9a: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase fr...

Basic information

• Entry: Database: PDB / ID: 3e9a
• Title: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961
• Components: 2-dehydro-3-deoxyphosphooctonate aldolase
• Keywords: TRANSFERASE / 2-dehydro-3-deoxyphosphooctonate aldolase / 3-deoxy-8-phosphooctulonate synthase / Lipopolysaccharide biosynthesis / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function:

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

Domain/homology:

3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Component:

2-dehydro-3-deoxyphosphooctonate aldolase / 2-dehydro-3-deoxyphosphooctonate aldolase

• Biological species: Vibrio cholerae O1 biovar El tor (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.8 Å
• Authors: Nocek, B. / Mulligan, R. / Kwon, K. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
• Citation: Journal: To be Published; Title: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961; Authors: Nocek, B. / Mulligan, R. / Kwon, K. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 21, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

Summary:

• 31.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	31,181	2
Polymers	31,085	1
Non-polymers	96	1
Water	3,045	169

1

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

Summary:

• defined by software
• 125 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	124,723	8
Polymers	124,339	4
Non-polymers	384	4
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1
crystal symmetry operation	3_655	-x+1,y,-z	1
crystal symmetry operation	4_555	x,-y,-z	1

Calculated values:

Buried area	14270 Å2
ΔGint	-138 kcal/mol
Surface area	36210 Å2
Method	PISA

2

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

Summary:

• defined by software
• 62.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	62,362	4
Polymers	62,169	2
Non-polymers	192	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_655	-x+1,y,-z	1

Calculated values:

Buried area	3820 Å2
ΔGint	-57 kcal/mol
Surface area	21420 Å2
Method	PISA

3

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase

hetero molecules

Summary:

• defined by software
• 62.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	62,362	4
Polymers	62,169	2
Non-polymers	192	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_555	x,-y,-z	1

Calculated values:

Buried area	3420 Å2
ΔGint	-42 kcal/mol
Surface area	21820 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	117.187, 117.187, 117.187
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

Components on special symmetry positions

ID	Model	Components
1	1	A-313- HOH
2	1	A-447- HOH

• Details: authors state that the biological assembly is unknown

Components

#1: Protein

A 2-dehydro-3-deoxyphosphooctonate aldolase / Phospho-2-dehydro-3-deoxyoctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase / KDO-8-phosphate synthetase / KDO 8-P synthase / KDOPS

Details:

Mass: 31084.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El tor (bacteria)
Strain: N16961 / Gene: kdsA, VC_2175 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KQ29, UniProt: A5F692*PLUS, 3-deoxy-8-phosphooctulonate synthase

#2: Chemical

A-284 ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.16 ų/Da / Density % sol: 42.98 %
• Crystal grow: Temperature: 291 K / pH: 6.5 ; Details: 0.05 Ammonium sulfate 0.05 bis-tris 30% pentaerythritol ethoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794
• Detector: Type: SBC-3 / Detector: CCD / Date: Aug 6, 2008 / Details: MIRRORS
• Radiation: Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9794 Å / Relative weight: 1
• Reflection: Resolution: 1.8→40 Å / Num. obs: 24922 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 20.3 % / B_iso Wilson estimate: 28.4 Ų / R_merge(I) obs: 0.082 / R_sym value: 0.78 / Net I/σ(I): 40
• Reflection shell: Resolution: 1.8→1.83 Å / Redundancy: 19.8 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing
CCP4		phasing

Refinement

Method to determine structure: molecular replacement
Starting model: 1O60

1o60

Resolution: 1.8→40 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.953 / SU B: 5.523 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.215	1245	5.1 %	RANDOM
Rwork	0.176	-	-	-
obs	0.178	23054	97.5 %	-
all	-	23054	-	-

• 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: 16.59 Ų

Refinement step

Cycle: LAST / Resolution: 1.8→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2108	0	5	169	2282

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	2159
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1466
X-RAY DIFFRACTION	r_angle_refined_deg	1.726	1.969	2919
X-RAY DIFFRACTION	r_angle_other_deg	1	3	3605
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.059	5	277
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.98	24.891	92
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.827	15	382
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.548	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	332
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2393
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	405
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	452
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	1536
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1055
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	1057
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	134
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.196	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.238	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.313	0.2	22
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.256	1.5	1777
X-RAY DIFFRACTION	r_mcbond_other	0.347	1.5	557
X-RAY DIFFRACTION	r_mcangle_it	1.499	2	2213
X-RAY DIFFRACTION	r_scbond_it	2.507	3	880
X-RAY DIFFRACTION	r_scangle_it	3.462	4.5	704
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.85 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.306	86	-
Rwork	0.229	1659	-
obs	-	-	97 %

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	35.0429	-0.2254	-22.2838	0.5071	0.896	15.2909	-0.0868	-1.0575	-0.6347	0.2373	0.5201	0.2516	0.0885	1.0451	-0.4332	0.179	0.1376	-0.0228	0.1719	0.0318	0.0401	51.183	23.4712	-18.1452
2	3.6249	0.7974	-0.6851	4.3535	-2.4154	5.3871	0.0601	0.1289	0.197	0.0522	0.2109	0.2266	-0.7235	-0.5254	-0.2709	0.1886	0.1637	0.0554	0.1005	0.0646	0.0483	39.2154	26.9122	-8.3159
3	1.7476	0.5003	-1.1113	1.8689	0.0748	2.5092	-0.0015	-0.1399	0.0367	0.3233	-0.0091	0.2277	-0.2302	-0.2802	0.0106	0.1676	0.13	0.1225	0.1135	0.039	0.0793	35.9232	21.6921	11.5214
4	1.4474	1.6142	-0.0813	4.753	0.7047	1.2244	0.0562	-0.0863	0.1128	0.3685	0.0315	0.2491	-0.3475	-0.3272	-0.0877	0.1686	0.1427	0.0979	0.0657	0.0414	0.0583	37.1114	24.3214	9.284
5	3.7918	-2.6358	5.9304	17.5269	-0.3576	10.1781	-0.1396	0.2005	0.535	1.8313	0.039	0.2063	0.1569	-0.2065	0.1005	0.2491	0.0387	0.2344	0.2979	0.1044	0.1036	28.6116	8.0391	13.891
6	5.6947	2.4065	0.0432	8.5137	-2.3032	6.9205	0.3381	0.2517	0.7401	-0.416	-0.3294	0.813	-0.6835	-0.5685	-0.0087	0.0424	0.2375	0.1642	0.135	-0.0092	0.1795	25.9205	26.0893	9.5123
7	2.644	0.9864	0.8058	3.8327	1.7085	2.0688	0.0048	-0.023	0.1017	0.0224	-0.0312	0.5768	-0.1975	-0.5201	0.0265	-0.0047	0.1095	0.0533	0.2144	0.0723	0.1511	27.7292	14.739	1.224
8	3.1393	0.6387	1.6182	6.3281	0.1299	1.7184	0.1219	0.122	-0.054	-0.0739	0.0561	0.2021	0.1344	-0.2631	-0.178	0.0241	0.0325	0.0153	0.1535	0.0589	0.0716	34.3295	5.5101	-4.2906
9	5.5008	-1.3253	1.0837	0.7022	-0.4412	2.3401	0.1711	0.1839	-0.1172	-0.1399	0.0238	0.2264	-0.099	-0.2306	-0.1949	0.061	0.0666	0.0027	0.134	0.0696	0.122	35.4522	11.9949	-4.7993
10	6.1048	-0.5152	2.7588	0.8061	-0.4791	1.3263	0.0707	0.3014	-0.4109	-0.2601	0.0799	0.1002	0.1426	-0.0966	-0.1506	0.1476	0.0516	-0.0379	0.1329	0.0189	0.0696	41.5117	7.47	-11.6295
11	6.7691	3.0744	4.1007	5.1331	8.2522	13.4107	0.1708	0.2095	0.5403	-0.4064	-0.2678	0.3308	-0.8449	-0.8476	0.097	0.1169	0.1201	-0.0391	0.1718	0.0984	0.086	33.5966	16.1062	-11.5865
12	5.3828	-2.6152	1.2686	4.054	-0.8655	0.3213	0.0026	-0.0884	-0.1318	-0.0861	0.0516	-0.0517	-0.0756	-0.0919	-0.0541	0.1125	0.0382	0.0246	0.077	0.0154	0.0741	49.7502	8.6192	0.1729
13	2.1794	1.8884	-2.4969	9.2017	2.8577	6.2104	0.1698	0.061	-0.0079	1.0472	-0.0452	0.3196	-0.1765	-0.0851	-0.1246	0.1004	-0.0131	-0.0157	0.0436	-0.0062	0.0997	54.2896	2.3422	6.2555
14	4.0092	-0.8415	-0.3231	0.3979	-0.3389	0.7737	0.1951	0.0776	-0.0813	-0.0166	0.0611	0.0645	-0.1618	-0.1167	-0.2563	0.2065	0.0307	0.0358	0.0502	0.0103	0.061	53.4153	14.6684	-6.8699
15	2.5506	-1.4425	2.6493	1.4493	-2.5145	9.9328	0.0864	0.0822	-0.0753	-0.0256	0.0094	0.155	-0.3082	-0.1405	-0.0958	0.117	0.0651	0.0287	0.04	0.0188	0.0691	46.203	16.5133	-4.6869
16	4.439	-3.8352	-4.0298	6.4348	9.0238	13.4988	0.2947	-0.7811	-0.3377	1.0346	0.3589	-0.2775	1.3313	0.1205	-0.6536	0.3827	-0.0117	-0.0028	0.2144	0.0939	0.1252	51.4074	12.4137	11.7599
17	4.859	-0.8667	-1.5636	7.0014	-0.8692	6.3075	-0.0931	-0.4274	0.092	0.3396	0.1704	0.1621	-0.098	0.0874	-0.0773	0.1767	0.038	0.0735	0.0566	-0.0133	0.043	55.417	19.9105	9.1912
18	2.8831	0.1979	-0.7294	0.9019	-0.1928	1.0872	-0.048	-0.1131	0.0416	0.0223	0.0737	0.0312	-0.2992	-0.0393	-0.0257	0.1719	0.0672	0.053	0.0512	0.0138	0.0566	48.4629	21.2862	1.0025
19	10.4995	7.3341	-3.1795	19.124	-6.8404	2.487	0.9221	-0.4235	-0.3662	1.1116	-0.6754	-0.3413	-0.3452	-0.1547	-0.2467	0.4053	-0.0197	-0.0104	0.0902	0.0501	-0.0571	41.5202	15.0901	19.7819
20	1.4184	0.5491	-0.4123	0.771	-0.1155	2.1518	0.1323	0.0131	0.0953	0.0339	0.0626	0.1008	-0.2746	-0.0986	-0.1949	0.2137	0.0596	0.0416	-0.0198	0.0181	0.0354	52.5275	27.3413	1.8295

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 3
2	X-RAY DIFFRACTION	2	A	4 - 17
3	X-RAY DIFFRACTION	3	A	18 - 36
4	X-RAY DIFFRACTION	4	A	37 - 62
5	X-RAY DIFFRACTION	5	A	63 - 80
6	X-RAY DIFFRACTION	6	A	81 - 89
7	X-RAY DIFFRACTION	7	A	90 - 111
8	X-RAY DIFFRACTION	8	A	112 - 127
9	X-RAY DIFFRACTION	9	A	128 - 141
10	X-RAY DIFFRACTION	10	A	142 - 157
11	X-RAY DIFFRACTION	11	A	158 - 164
12	X-RAY DIFFRACTION	12	A	165 - 173
13	X-RAY DIFFRACTION	13	A	174 - 178
14	X-RAY DIFFRACTION	14	A	179 - 188
15	X-RAY DIFFRACTION	15	A	189 - 202
16	X-RAY DIFFRACTION	16	A	203 - 218
17	X-RAY DIFFRACTION	17	A	219 - 226
18	X-RAY DIFFRACTION	18	A	227 - 239
19	X-RAY DIFFRACTION	19	A	240 - 251
20	X-RAY DIFFRACTION	20	A	252 - 283