PDB-3si9: Crystal structure of Dihydrodipicolinate Synthase from Bartonella...

ID or keywords:

Entry

Database: PDB / ID: 3si9

Title

Crystal structure of Dihydrodipicolinate Synthase from Bartonella Henselae

Components

Dihydrodipicolinate synthase

Keywords

LYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TIM Barrel

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

Bartonella henselae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Staker, B.L. / Abendroth, J. / Sankaran, B.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2. ...
Authors: Naqvi, K.F. / Staker, B.L. / Dobson, R.C. / Serbzhinskiy, D. / Sankaran, B. / Myler, P.J. / Hudson, A.O.

History

Deposition	Jun 17, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 2, 2016	Group: Database references
Revision 1.3	Sep 13, 2023	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_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_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

-
Download

PDBx/mmCIF format	3si9.cif.gz	453.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3si9.ent.gz	375.8 KB	Display	PDB format
PDBx/mmJSON format	3si9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3si9_validation.pdf.gz	462.5 KB	Display	wwPDB validaton report
Full document	3si9_full_validation.pdf.gz	466.3 KB	Display
Data in XML	3si9_validation.xml.gz	45.8 KB	Display
Data in CIF	3si9_validation.cif.gz	66.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/si/3si9 ftp://data.pdbj.org/pub/pdb/validation_reports/si/3si9	HTTPS FTP

-
Related structure data

Related structure data	2rfgS S: Starting model for refinement
Similar structure data	2vc6-1 7loy-2 4i7v-d 7lvl-2 4xky-d 7loy-1 1xxx-2 6xgs-d 4i7w-1 2yxg-d 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: BaheA.01563.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Dihydrodipicolinate synthase

B: Dihydrodipicolinate synthase

C: Dihydrodipicolinate synthase

D: Dihydrodipicolinate synthase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	79.963, 106.334, 136.253
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

#1: Protein	Dihydrodipicolinate synthase / DHDPS Mass: 33810.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: HOUSTON-1 / Gene: dapA, BH05000 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G468, dihydrodipicolinate synthase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG 4000, 100MM SODIUM CITRATE TRIBASIC PH 5.5, 25.2 MG/ML PROTEIN BAHEA.01563.A.A1.PS00847, WIZARD III/IV CONDITION B5, 218706B5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2011

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9774	1
2	0.9774	1

Reflection

Resolution: 2.1→50 Å / Num. obs: 68289 / % possible obs: 99.8 % / Redundancy: 6.1 % / R_merge(I) obs: 0.09 / Net I/σ(I): 18.3

Reflection shell

Resolution: 2.1→2.14 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.418 / Mean I/σ(I) obs: 3.5 / % possible all: 100

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2RFG

2rfg

Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.927 / SU B: 12.738 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.233	3445	5.1 %	RANDOM
R_work	0.183	-	-	-
obs	0.186	67983	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 22.38 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.56 Å²	0 Å²	0 Å²
2-	-	-1.59 Å²	0 Å²
3-	-	-	1.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8672	0	36	560	9268

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	8946
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5910
X-RAY DIFFRACTION	r_angle_refined_deg	1.44	1.969	12163
X-RAY DIFFRACTION	r_angle_other_deg	1.017	3	14547
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.931	5	1194
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.722	24.418	335
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.904	15	1461
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.905	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	1450
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10065
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1671
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.535	1.5	5897
X-RAY DIFFRACTION	r_mcbond_other	0.137	1.5	2397
X-RAY DIFFRACTION	r_mcangle_it	0.923	2	9498
X-RAY DIFFRACTION	r_scbond_it	1.653	3	3049
X-RAY DIFFRACTION	r_scangle_it	2.523	4.5	2662
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	247	-
R_work	0.227	4586	-
obs	-	-	97.24 %

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	1.321	0.1774	0.5448	0.4194	0.1103	2.1313	-0.0204	0.0946	-0.0046	-0.0298	-0.0276	-0.1094	0.0436	0.1145	0.048	0.141	0.0421	0.0445	0.1474	0.0135	0.1846	23.5927	90.4313	9.8958
2	0.3179	-0.0074	-0.1989	0.7945	0.1465	0.9491	0.0627	0.0243	0.0888	-0.0451	-0.0406	-0.0883	-0.1581	0.0494	-0.0221	0.1441	0.0087	0.0225	0.1274	0.0326	0.1831	17.1465	107.8995	18.4819
3	3.6475	0.9728	-1.5708	5.9798	-1.4958	3.9292	0.1489	0.1604	0.1411	-0.0304	-0.0757	-0.0285	-0.5314	-0.0694	-0.0732	0.2062	0.0316	-0.008	0.147	0.0216	0.1588	0.5914	109.4662	12.3246
4	1.2878	0.207	0.147	1.579	-0.0982	1.0686	-0.0179	0.2234	0.0156	-0.1687	0.0053	-0.022	-0.085	-0.0671	0.0126	0.1621	0.0259	0.0265	0.1828	0.012	0.1174	3.8264	95.062	4.9644
5	0.3945	0.085	0.2007	1.2509	-0.1348	0.6089	0.0593	0.0183	-0.0953	-0.0908	-0.0314	-0.0123	0.1274	-0.0467	-0.0279	0.1789	0.0246	0.0218	0.1082	-0.0066	0.1732	10.8132	80.6788	17.7446
6	2.4107	5.875	2.3262	8.8776	-0.0469	6.5836	0.2499	0.3332	-0.4535	-0.2641	0.436	0.0893	1.2263	0.1668	-0.6859	0.3024	0.0261	0.0113	0.0341	-0.0678	0.3406	4.1628	76.0794	8.1047
7	1.8493	-0.4968	-0.2996	1.348	-0.9063	2.333	0.0207	0.1479	0.0563	0.0759	-0.0573	0.0634	-0.018	-0.2052	0.0366	0.1	0.0254	0.0129	0.2251	0.0482	0.2032	-30.2484	109.3064	15.5313
8	0.4724	-0.004	0.545	1.439	1.4017	1.8559	0.0778	-0.0771	0.0103	-0.003	-0.1162	0.1316	0.0413	-0.2087	0.0384	0.0741	0.0109	0.0252	0.2175	0.0289	0.2138	-31.613	103.1339	23.671
9	0.6431	-0.5532	1.785	1.6641	-1.4483	5.5251	0.0621	0.0218	-0.0645	-0.0448	0.1187	0.1802	0.0906	-0.3771	-0.1808	0.0595	0.0047	0.0039	0.2302	0.014	0.1672	-32.6678	95.8103	21.0389
10	0.5498	0.1383	0.0105	0.5808	-0.1144	0.7605	0.0654	0.0937	-0.0738	0.0496	-0.0589	-0.0001	0.1577	-0.0676	-0.0065	0.1498	-0.0152	0.0098	0.1452	-0.0173	0.1708	-19.8774	88.2283	24.3354
11	1.0713	-0.07	-0.0418	0.3835	0.126	0.575	0.0492	0.1827	0.0163	-0.0765	0.0023	-0.028	0.0056	-0.0072	-0.0515	0.1563	0.0082	0.0205	0.1918	0.0089	0.1335	-12.4616	99.8325	9.0389
12	0.9116	0.4277	-0.4305	2.3526	0.2047	1.4753	-0.0151	0.0522	0.2435	-0.339	0.0523	-0.2108	-0.2121	-0.0266	-0.0372	0.1666	0.015	0.0394	0.0989	0.0347	0.1832	-17.8795	117.816	20.6309
13	4.2556	2.7877	-3.2891	3.8821	-1.9112	6.8898	-0.125	0.1191	-0.1301	-0.019	0.1041	-0.2867	-0.0887	-0.0981	0.0209	0.0791	0.0058	-0.0487	0.1539	-0.008	0.2598	26.424	108.3803	44.9198
14	0.2622	-0.0019	0.1	0.5907	0.0986	0.792	0.051	-0.02	0.0515	0.0417	-0.0342	-0.1256	0.0281	0.1355	-0.0168	0.103	-0.0064	-0.0009	0.1483	0.0153	0.2076	28.2425	100.9356	43.3636
15	0.1362	-0.1671	0.2476	0.4167	0.1634	1.4662	0.0482	-0.0525	-0.0953	-0.0181	0.0187	-0.0343	0.1083	0.0036	-0.0669	0.131	-0.0157	-0.0088	0.1392	0.0453	0.217	16.6244	87.102	41.0781
16	1.7994	0.5361	-0.3073	1.7554	0.0453	-0.1164	-0.0249	-0.0693	-0.0614	0.0145	0.0206	0.0257	0.0225	0.0021	0.0043	0.1911	-0.0152	-0.0099	0.1628	0.0152	0.1343	9.053	93.6865	51.9287
17	0.4838	0.2357	-0.1913	0.559	-0.0142	0.9739	0.0316	-0.0942	0.1525	0.0659	-0.0015	0.0295	0.0054	0.0281	-0.0301	0.1459	-0.005	-0.0144	0.1183	-0.0102	0.1946	14.496	111.6646	49.777
18	2.3155	1.5081	0.5388	2.9863	-5.669	16.0139	-0.0057	-0.0404	0.3742	0.2881	-0.0235	0.1977	-0.6926	-0.0531	0.0292	0.1963	0.0466	0.0315	0.0565	-0.0276	0.235	10.9774	122.1553	47.4896
19	1.8698	0.7119	0.8289	1.5918	-0.3877	2.6884	0.0019	-0.1166	0.0759	0.0622	0.0123	0.2022	0.1373	-0.0434	-0.0143	0.1823	-0.031	0.0556	0.168	0.0086	0.1457	-23.3115	89.9112	56.2386
20	0.3017	0.1071	0.0877	0.5895	-0.0865	0.8033	0.0359	-0.0552	0.0743	0.0361	-0.0111	0.0885	-0.0104	-0.1551	-0.0248	0.1145	-0.0247	0.0351	0.1613	-0.0171	0.1813	-22.4148	105.4805	46.8415
21	2.2841	-0.4699	-0.6572	2.2465	0.252	0.1977	0.0652	-0.0274	0.1978	0.2635	0.0023	-0.1922	-0.0327	-0.0482	-0.0675	0.1917	-0.0251	0.0142	0.1786	-0.0148	0.1444	-6.563	108.781	51.1148
22	0.7309	0.0679	0.294	1.5717	0.5971	0.3593	0.0414	-0.1719	0.0334	-0.0208	-0.0079	0.0406	-0.0468	-0.0548	-0.0336	0.1611	-0.0389	0.0153	0.1988	-0.006	0.1366	-8.5537	98.1513	56.3677
23	1.0399	-0.1042	0.5048	0.2736	-0.0131	0.9404	0.0821	-0.0758	-0.0971	0.1244	-0.0191	0.0178	0.1479	-0.0012	-0.063	0.1941	-0.0472	-0.0049	0.1358	0.023	0.1294	-10.2543	85.0872	52.3008
24	5.4064	8.299	-5.6066	13.8816	-1.1595	9.0949	0.0085	-0.1489	-0.855	0.6743	-0.5235	-0.6678	0.4308	-0.118	0.5149	0.2951	-0.0175	-0.0099	0.0531	0.116	0.2576	-7.1587	77.0463	58.1218

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 75
2	X-RAY DIFFRACTION	2	A	76 - 170
3	X-RAY DIFFRACTION	3	A	171 - 184
4	X-RAY DIFFRACTION	4	A	185 - 238
5	X-RAY DIFFRACTION	5	A	239 - 287
6	X-RAY DIFFRACTION	6	A	288 - 297
7	X-RAY DIFFRACTION	7	B	4 - 40
8	X-RAY DIFFRACTION	8	B	41 - 66
9	X-RAY DIFFRACTION	9	B	67 - 97
10	X-RAY DIFFRACTION	10	B	98 - 170
11	X-RAY DIFFRACTION	11	B	171 - 245
12	X-RAY DIFFRACTION	12	B	246 - 296
13	X-RAY DIFFRACTION	13	C	4 - 24
14	X-RAY DIFFRACTION	14	C	25 - 113
15	X-RAY DIFFRACTION	15	C	114 - 170
16	X-RAY DIFFRACTION	16	C	171 - 209
17	X-RAY DIFFRACTION	17	C	210 - 278
18	X-RAY DIFFRACTION	18	C	279 - 296
19	X-RAY DIFFRACTION	19	D	4 - 50
20	X-RAY DIFFRACTION	20	D	51 - 160
21	X-RAY DIFFRACTION	21	D	161 - 184
22	X-RAY DIFFRACTION	22	D	185 - 218
23	X-RAY DIFFRACTION	23	D	219 - 288
24	X-RAY DIFFRACTION	24	D	289 - 297

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi