PDB-6mqh: Crystal structure of 4-hydroxy-tetrahydrodipicolinate synthase (H...

ID or keywords:

Entry

Database: PDB / ID: 6mqh

Title

Crystal structure of 4-hydroxy-tetrahydrodipicolinate synthase (HTPA synthase) from Burkholderia mallei

Components

4-hydroxy-tetrahydrodipicolinate synthase

Dihydrodipicolinate synthase

Keywords

LYASE / SSGCID /

Burkholderia multivorans /

4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase /

dapA /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

4-hydroxy-tetrahydrodipicolinate synthase /

4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate /

cytoplasm
Similarity search - Function

Biological species

Burkholderia mallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of 4-hydroxy-tetrahydrodipicolinate synthase (HTPA synthase) from Burkholderia mallei
Authors: Abendroth, J. / Conrady, D.G. / Lorimer, D.D. / Horanyi, P.E. / Edwards, T.E.

History

Deposition	Oct 9, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2018	Provider: repository / Type: Initial release
Revision 2.0	Dec 12, 2018	Group: Atomic model / Data collection / Refinement description Category: atom_site / refine_ls_restr / Item: _atom_site.occupancy
Revision 2.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6mqh.cif.gz	247.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6mqh.ent.gz	198.6 KB	Display	PDB format
PDBx/mmJSON format	6mqh.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/6mqh ftp://data.pdbj.org/pub/pdb/validation_reports/mq/6mqh	HTTPS FTP

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Related structure data

Similar structure data	3ird-1 5f1v-d 4r53-d 4mlj-d 2rfg-d 4m19-d 3pb2-1 4mlr-1 3a5f-1 5f1u-d 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: BumaA.0.1563.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 4-hydroxy-tetrahydrodipicolinate synthase

B: 4-hydroxy-tetrahydrodipicolinate synthase

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

1

A: 4-hydroxy-tetrahydrodipicolinate synthase

B: 4-hydroxy-tetrahydrodipicolinate synthase

A: 4-hydroxy-tetrahydrodipicolinate synthase

B: 4-hydroxy-tetrahydrodipicolinate synthase

defined by author&software
Evidence: gel filtration
131 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	150.870, 53.930, 78.630
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-668- HOH
2	1	A-695- HOH
3	1	B-416- HOH

#1: Protein	4-hydroxy-tetrahydrodipicolinate synthase / Dihydrodipicolinate synthase / HTPA synthase Mass: 32865.863 Da / Num. of mol.: 2 / Fragment: BumaA.01530.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia mallei (strain ATCC 23344) (bacteria) Strain: ATCC 23344 / Gene: dapA, BMA1678 / Plasmid: BumaA.01563.a.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H2WFM6, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

4-hydroxy-tetrahydrodipicolinate synthase /

Dihydrodipicolinate synthase / HTPA synthase

Mass: 32865.863 Da / Num. of mol.: 2 / Fragment: BumaA.01530.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia mallei (strain ATCC 23344) (bacteria)
Strain: ATCC 23344 / Gene: dapA, BMA1678 / Plasmid: BumaA.01563.a.B1
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H2WFM6,

4-hydroxy-tetrahydrodipicolinate synthase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.44 Å³/Da / Density % sol: 49.6 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23.87 mg/mL BumaA.01563.a.B1.PW38480 + 5 mM AMPPNP + 5 mM magnesium chloride against Molecular Dimensions Morpheus screen, E3 (10% w/v PEG4000, 20% v/v glycerol, 30 mM diethyleneglycol, 30 ...Details: 23.87 mg/mL BumaA.01563.a.B1.PW38480 + 5 mM AMPPNP + 5 mM magnesium chloride against Molecular Dimensions Morpheus screen, E3 (10% w/v PEG4000, 20% v/v glycerol, 30 mM diethyleneglycol, 30 mM triethyleneglycol, 30 mM tetraethyleneglycol, 30 mM pentaethyleneglycol, 100 mM MES/imidazole, pH 6.5), cryoprotecion: direct, tray 301751e3, puck egq4-8, for phasing, a crystal from an apo setup of the same protein from Rigaku Reagents JCSG+ screen C4 (10% PEG6000, 100 mM HEPES free acid/NaOH) was incubated for 10 seconds each in 12.5% 2.5 M sodium iodide in ethylene glycol and in 25% 2.5 M sodium iodide in ethylene glycol (625 mM final sodium iodide concentration) and directly vitrified, puck: OVZ1-3

Crystal

Density Matthews: 2.44 Å³/Da / Density % sol: 49.6 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23.87 mg/mL BumaA.01563.a.B1.PW38480 + 5 mM AMPPNP + 5 mM magnesium chloride against Molecular Dimensions Morpheus screen, E3 (10% w/v PEG4000, 20% v/v glycerol, 30 mM diethyleneglycol, 30 ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date	Details
RAYONIX MX-300	1	CCD	Aug 8, 2018
RIGAKU SATURN 944+	2	CCD	Sep 12, 2018	RIGAKU VARIMAX

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	diamond (111)	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.7→44.474 Å / Num. obs: 71091 / % possible obs: 99.5 % / Redundancy: 6.081 % / B_iso Wilson estimate: 25.072 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.067 / Χ²: 1.021 / Net I/σ(I): 19.01

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	6.157	0.482	3.99	5203	0.915	0.526	100
1.74-1.79	6.155	0.378	5.03	5108	0.948	0.414	100
1.79-1.84	6.171	0.313	5.94	4914	0.964	0.342	100
1.84-1.9	6.159	0.272	6.88	4789	0.976	0.298	99.7
1.9-1.96	5.876	0.189	10.36	4422	0.984	0.208	94.2
1.96-2.03	6.176	0.156	11.38	4506	0.991	0.17	100
2.03-2.11	6.17	0.121	14.13	4354	0.993	0.133	100
2.11-2.19	6.169	0.102	16.45	4214	0.994	0.111	100
2.19-2.29	5.76	0.091	18.08	3976	0.994	0.101	98.8
2.29-2.4	6.162	0.075	20.62	3878	0.997	0.082	100
2.4-2.53	6.171	0.066	23.42	3700	0.997	0.072	100
2.53-2.69	6.158	0.059	25.74	3506	0.998	0.064	100
2.69-2.87	6.145	0.051	28.75	3280	0.998	0.056	100
2.87-3.1	6.127	0.044	32.8	3071	0.998	0.048	99.9
3.1-3.4	6.099	0.039	36.79	2871	0.998	0.042	99.9
3.4-3.8	5.979	0.036	39.52	2580	0.998	0.039	100
3.8-4.39	6	0.032	42.09	2288	0.999	0.035	99.9
4.39-5.38	5.945	0.031	42.95	1975	0.999	0.034	100
5.38-7.6	5.791	0.033	41	1547	0.999	0.037	99.9
7.6-44.474	5.221	0.032	42.87	909	0.999	0.035	98.4

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Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.7→44.474 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.92

	R_factor	Num. reflection	% reflection
R_free	0.1948	1957	2.76 %
R_work	0.1675	-	-
obs	0.1683	70904	99.23 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 74.78 Å² / B_iso mean: 21.7755 Å² / B_iso min: 6.71 Å²

Refinement step

Cycle: final / Resolution: 1.7→44.474 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4340	0	0	805	5145
B_iso mean	-	-	-	33.39	-
Num. residues	-	-	-	-	586

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4501
X-RAY DIFFRACTION	f_angle_d	0.95	6141
X-RAY DIFFRACTION	f_chiral_restr	0.063	738
X-RAY DIFFRACTION	f_plane_restr	0.007	796
X-RAY DIFFRACTION	f_dihedral_angle_d	12.457	2763

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7425	0.2453	144	0.1852	4886	5030	100
1.7425-1.7897	0.1896	137	0.1808	4882	5019	100
1.7897-1.8423	0.2383	142	0.1771	4890	5032	100
1.8423-1.9018	0.2298	140	0.1905	4875	5015	100
1.9018-1.9698	0.3103	129	0.2934	4462	4591	91
1.9698-2.0486	0.2119	151	0.1663	4916	5067	100
2.0486-2.1419	0.209	157	0.1614	4907	5064	100
2.1419-2.2548	0.3017	134	0.25	4932	5066	99
2.2548-2.396	0.2059	138	0.1788	4916	5054	100
2.396-2.581	0.1809	127	0.1613	4978	5105	100
2.581-2.8407	0.1962	128	0.1587	4982	5110	100
2.8407-3.2517	0.1637	143	0.1509	4994	5137	100
3.2517-4.0963	0.1609	158	0.1347	5043	5201	100
4.0963-44.4896	0.1499	129	0.1419	5284	5413	100

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	1.3568	-0.1172	0.1314	0.809	0.1933	2.626	0.0333	-0.4064	0.1704	0.1148	0.0031	-0.1855	-0.1597	0.4069	-0.0518	0.1652	-0.0419	-0.0428	0.3122	-0.0741	0.183	25.855	13.6455	69.3467
2	0.9726	0.1237	0.0673	0.8815	0.4253	1.536	-0.0424	-0.2692	-0.0989	0.0749	0.032	-0.1622	0.15	0.291	-0.0179	0.1157	0.0328	-0.0225	0.2063	0.0206	0.1202	22.5221	-3.9816	62.4994
3	0.7114	0.3985	-0.2889	1.098	-0.217	1.1148	0.0139	-0.2706	0.0624	0.1202	-0.0069	-0.0262	-0.0718	0.0295	-0.0081	0.1374	0.003	-0.0163	0.2245	-0.0357	0.1131	10.0859	9.0901	71.0827
4	3.6998	-0.1271	2.0308	4.7164	-0.6582	1.7907	-0.2281	-0.6467	0.5844	0.3112	0.2552	0.1112	-0.956	-0.5006	0.0011	0.3196	0.0855	0.0097	0.2559	-0.1055	0.2597	5.6599	25.7172	66.4487
5	1.895	-0.1114	0.6568	0.771	-0.5354	2.8958	-0.0124	0.0864	0.0129	-0.0725	-0.0224	-0.1146	-0.0083	0.26	0.0363	0.0647	0.0007	0.0185	0.0921	-0.0065	0.1287	29.014	-3.3464	32.6207
6	1.0087	-0.2139	-0.2853	0.5097	0.119	1.161	0.0391	-0.0103	0.1444	0.0161	-0.0074	-0.0823	-0.1805	0.1125	-0.0244	0.107	-0.0259	0.0071	0.066	0.0039	0.1339	19.46	12.0052	39.5836
7	1.2348	-0.4532	0.2238	0.7338	-0.2068	1.038	0.0049	0.1211	-0.0819	-0.0281	-0.0363	0.0093	0.0871	0.0096	0.0115	0.0785	-0.0089	0.0171	0.0733	-0.0067	0.1061	12.6429	-4.8828	31.032
8	2.1079	0.43	0.5365	4.3124	-1.251	1.482	-0.342	0.0404	-0.3314	-0.5145	0.0837	0.1485	0.7935	-0.3823	0.0433	0.3765	-0.0908	0.0508	0.0766	-0.0305	0.2492	14.6106	-21.9737	34.9502

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 76 )	A	8 - 76
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 175 )	A	77 - 175
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 176 through 283 )	A	176 - 283
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 284 through 300 )	A	284 - 300
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 76 )	B	8 - 76
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 77 through 175 )	B	77 - 175
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 176 through 283 )	B	176 - 283
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 284 through 300 )	B	284 - 300

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