PDB-4ly8: dihydrodipicolinate synthase from C. jejuni with pyruvate bound t...

ID or keywords:

Entry

Database: PDB / ID: 4ly8

Title

dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site

Components

4-hydroxy-tetrahydrodipicolinate synthase

Keywords

LYASE / schiff-base / aldolase / TIM barrel / type 1 aldolase catalysing condensation of pyruvate and S-aspartate-B-semi-aldehyde

Function / homology

Function and homology information

(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Conly, C.J.T.

Citation

Journal: Biochemistry / Year: 2014
Title: Tyrosine 110 Plays a Critical Role in Regulating the Allosteric Inhibition of Campylobacter jejuni Dihydrodipicolinate Synthase by Lysine.
Authors: Conly, C.J. / Skovpen, Y.V. / Li, S. / Palmer, D.R. / Sanders, D.A.

History

Deposition	Jul 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ly8.cif.gz	496.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4ly8_validation.pdf.gz	491.8 KB	Display	wwPDB validaton report
Full document	4ly8_full_validation.pdf.gz	505.2 KB	Display
Data in XML	4ly8_validation.xml.gz	27.9 KB	Display
Data in CIF	4ly8_validation.cif.gz	42.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ly/4ly8 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4ly8	HTTPS FTP

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Related structure data

Related structure data	4m19C 4mljC 4mlrC 4r53C C: citing same article (ref.)
Similar structure data	6u01-2 4r53-d 6tzu-1 6u01-1 4mlj-d 6tzu-2 3m5v-d 3ler-d 4ur8-d 2a6n-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 4-hydroxy-tetrahydrodipicolinate synthase

B: 4-hydroxy-tetrahydrodipicolinate synthase

C: 4-hydroxy-tetrahydrodipicolinate synthase

D: 4-hydroxy-tetrahydrodipicolinate synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	81.254, 101.404, 147.960
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase Mass: 33752.746 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0806, dapA / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

#1: Protein

4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase

Mass: 33752.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0806, dapA / Plasmid: pQE-80L / Production host:

Escherichia coli (E. coli) / Strain (production host): XL1-blue
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 6 types, 652 molecules

#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.26 Å³/Da / Density % sol: 45.51 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18% PEG4000, 0.25 mM sodium acetate, 0.1 mM TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08B1-1 / Wavelength: 0.9796 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 12, 2012

Radiation

Monochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9796 Å / Relative weight: 1

Reflection

Resolution: 1.6→43.01 Å / Num. all: 158522 / Num. obs: 158522 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.59 % / B_iso Wilson estimate: 18.13 Å² / R_merge(I) obs: 0.129 / Χ²: 0.79 / Net I/σ(I): 5.8 / Scaling rejects: 194883

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	Χ²	% possible all
1.6-1.66	2.5	0.541	1.5	54428	14220	0.53	89.1
1.66-1.72	3.16	0.539	1.8	73174	15336	0.61	96.2
1.72-1.8	4.57	0.527	2.4	105564	15934	0.82	99.6
1.8-1.9	5.34	0.52	2.5	119626	15973	0.77	99.9
1.9-2.02	5.74	0.486	2.8	120200	16010	0.82	99.9
2.02-2.17	6.23	0.422	3.3	120559	16029	0.83	100
2.17-2.39	6.62	0.359	4	121365	16112	0.96	99.9
2.39-2.74	6.91	0.259	5.2	121778	16130	0.86	99.9
2.74-3.45	7.14	0.151	8.2	122323	16189	0.81	99.6
3.45-43.01	7.19	0.064	17.2	122578	16589	0.63	99.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
d*TREK	9.9.9.4L	data scaling
d*TREK	9.9.9.4L	data reduction
MOLREP		phasing
PHENIX	dev_1327	refinement
PDB_EXTRACT	3.11	data extraction
MxDC		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LY8

Resolution: 1.7→43.01 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7735 / SU ML: 0.31 / σ(F): 1.44 / Phase error: 29.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2555	6714	5 %	RANDOM
R_work	0.2091	-	-	-
all	0.2114	134227	-	-
obs	0.2114	134227	99.68 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 160.57 Å² / B_iso mean: 29.0138 Å² / B_iso min: 12.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→43.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9167	0	262	610	10039

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9629
X-RAY DIFFRACTION	f_angle_d	1.112	12896
X-RAY DIFFRACTION	f_chiral_restr	0.075	1464
X-RAY DIFFRACTION	f_plane_restr	0.005	1632
X-RAY DIFFRACTION	f_dihedral_angle_d	15.633	3691

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7193	0.4606	186	0.4546	4170	4356	98
1.7193-1.7396	0.4397	222	0.447	4162	4384	99
1.7396-1.7608	0.4491	223	0.4295	4222	4445	100
1.7608-1.7831	0.419	209	0.4105	4204	4413	100
1.7831-1.8065	0.3967	221	0.3966	4264	4485	100
1.8065-1.8313	0.4091	216	0.3758	4191	4407	100
1.8313-1.8574	0.3857	242	0.3522	4197	4439	100
1.8574-1.8852	0.3531	216	0.3331	4223	4439	100
1.8852-1.9146	0.3508	212	0.315	4242	4454	100
1.9146-1.946	0.3664	223	0.3141	4218	4441	100
1.946-1.9796	0.3479	240	0.2999	4219	4459	100
1.9796-2.0156	0.3181	231	0.2788	4202	4433	100
2.0156-2.0543	0.3385	210	0.2687	4232	4442	100
2.0543-2.0962	0.2995	210	0.2456	4262	4472	100
2.0962-2.1418	0.2781	231	0.2225	4259	4490	100
2.1418-2.1917	0.2605	232	0.2021	4211	4443	100
2.1917-2.2465	0.2502	226	0.1974	4241	4467	100
2.2465-2.3072	0.2304	223	0.1894	4235	4458	100
2.3072-2.3751	0.2347	224	0.1846	4260	4484	100
2.3751-2.4517	0.2379	237	0.1817	4241	4478	100
2.4517-2.5393	0.2557	235	0.1806	4251	4486	100
2.5393-2.641	0.2534	241	0.1727	4216	4457	100
2.641-2.7612	0.2476	200	0.1752	4295	4495	100
2.7612-2.9067	0.227	235	0.1743	4275	4510	100
2.9067-3.0888	0.2405	212	0.1702	4287	4499	100
3.0888-3.3272	0.2063	249	0.1789	4242	4491	99
3.3272-3.6619	0.224	213	0.1625	4307	4520	99
3.6619-4.1914	0.1921	197	0.1401	4328	4525	99
4.1914-5.2792	0.1956	228	0.1429	4337	4565	99
5.2792-43.0285	0.1869	270	0.1632	4520	4790	100

Refinement TLS params.

Method: refined / Origin x: -11.4091 Å / Origin y: 4.0266 Å / Origin z: 53.7265 Å

	11	12	13	21	22	23	31	32	33
T	0.175 Å²	0.0004 Å²	0.0008 Å²	-	0.1392 Å²	-0.0114 Å²	-	-	0.1756 Å²
L	0.5401 °²	-0.0484 °²	-0.0009 °²	-	0.6458 °²	-0.0031 °²	-	-	0.386 °²
S	-0.0069 Å °	-0.0384 Å °	-0.0153 Å °	0.1358 Å °	-0.0214 Å °	0.0261 Å °	0.0251 Å °	-0.0399 Å °	0.028 Å °

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	all	A	1 - 298
2	X-RAY DIFFRACTION	1	all	B	2 - 298
3	X-RAY DIFFRACTION	1	all	C	1 - 298
4	X-RAY DIFFRACTION	1	all	D	2 - 298
5	X-RAY DIFFRACTION	1	all	C	1 - 301
6	X-RAY DIFFRACTION	1	all	B	1 - 301
7	X-RAY DIFFRACTION	1	all	D	1 - 301
8	X-RAY DIFFRACTION	1	all	A	1 - 301
9	X-RAY DIFFRACTION	1	all	A	1 - 302
10	X-RAY DIFFRACTION	1	all	B	1 - 302
11	X-RAY DIFFRACTION	1	all	D	1 - 302
12	X-RAY DIFFRACTION	1	all	D	1 - 303
13	X-RAY DIFFRACTION	1	all	A	1 - 303
14	X-RAY DIFFRACTION	1	all	A	1 - 304
15	X-RAY DIFFRACTION	1	all	C	1 - 302
16	X-RAY DIFFRACTION	1	all	C	1 - 303
17	X-RAY DIFFRACTION	1	all	B	1 - 303
18	X-RAY DIFFRACTION	1	all	B	1 - 304
19	X-RAY DIFFRACTION	1	all	A	1 - 305
20	X-RAY DIFFRACTION	1	all	D	1 - 304
21	X-RAY DIFFRACTION	1	all	D	1 - 305
22	X-RAY DIFFRACTION	1	all	D	1 - 306
23	X-RAY DIFFRACTION	1	all	A	1 - 306
24	X-RAY DIFFRACTION	1	all	B	1 - 305
25	X-RAY DIFFRACTION	1	all	C	1 - 304
26	X-RAY DIFFRACTION	1	all	D	1 - 307
27	X-RAY DIFFRACTION	1	all	C	1 - 305
28	X-RAY DIFFRACTION	1	all	D	1 - 308
29	X-RAY DIFFRACTION	1	all	B	1 - 306
30	X-RAY DIFFRACTION	1	all	C	1 - 306
31	X-RAY DIFFRACTION	1	all	D	1 - 309
32	X-RAY DIFFRACTION	1	all	A - B	1 - 836
33	X-RAY DIFFRACTION	1	all	A	1 - 307
34	X-RAY DIFFRACTION	1	all	B	1 - 307
35	X-RAY DIFFRACTION	1	all	C	1 - 307
36	X-RAY DIFFRACTION	1	all	A	1 - 308
37	X-RAY DIFFRACTION	1	all	A	1 - 309
38	X-RAY DIFFRACTION	1	all	A	1 - 310
39	X-RAY DIFFRACTION	1	all	A	1 - 311
40	X-RAY DIFFRACTION	1	all	B	1 - 308
41	X-RAY DIFFRACTION	1	all	A	1 - 312
42	X-RAY DIFFRACTION	1	all	A	1 - 313
43	X-RAY DIFFRACTION	1	all	A	1 - 314
44	X-RAY DIFFRACTION	1	all	C	1 - 308
45	X-RAY DIFFRACTION	1	all	C	1 - 309
46	X-RAY DIFFRACTION	1	all	A	1 - 315
47	X-RAY DIFFRACTION	1	all	B	1 - 309

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