PDB-3qy9: The Crystal Structure of Dihydrodipicolinate reductase from Staph...

ID or keywords:

Entry

Database: PDB / ID: 3qy9

Title

The Crystal Structure of Dihydrodipicolinate reductase from Staphylococcus aureus

Components

Dihydrodipicolinate reductase

Keywords

OXIDOREDUCTASE / Rossmann Fold / Reductase / NADH / NADPH / Dihydrodipicolinate

Function / homology

Function and homology information

4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Girish, T.S. / Gopal, B.

Citation

Journal: Febs Lett. / Year: 2011
Title: Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB)
Authors: Girish, T.S. / Navratna, V. / Gopal, B.

History

Deposition	Mar 3, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 3, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2011	Group: Database references
Revision 1.2	Nov 1, 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

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Download

PDBx/mmCIF format	3qy9.cif.gz	396.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3qy9.ent.gz	326.9 KB	Display	PDB format
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Validation report

Summary document	3qy9_validation.pdf.gz	492.8 KB	Display	wwPDB validaton report
Full document	3qy9_full_validation.pdf.gz	502.4 KB	Display
Data in XML	3qy9_validation.xml.gz	43.4 KB	Display
Data in CIF	3qy9_validation.cif.gz	63 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/3qy9 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/3qy9	HTTPS FTP

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Related structure data

Related structure data	1arzS S: Starting model for refinement
Similar structure data	3ihp-1 3q3c-1 2i9p-d 5j9w-2 5mzu-d 5j9t-3 5j9w-1 4ywj-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: Dihydrodipicolinate reductase

B: Dihydrodipicolinate reductase

C: Dihydrodipicolinate reductase

D: Dihydrodipicolinate reductase

hetero molecules

110 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)	85.900, 112.440, 131.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Dihydrodipicolinate reductase / DHPR Mass: 26975.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: dapB / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HG24, EC: 1.3.1.26
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.95 Å³/Da / Density % sol: 58.24 %
Crystal grow	Temperature: 298 K / Method: microbatch under oil sitting drop / pH: 4.5 Details: 2.0M Ammonium sulfate, 0.2M Sodium actetate , pH 4.5, Microbatch under oil sitting drop, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2010 / Details: Mirror
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.8→29.64 Å / Num. obs: 115798 / % possible obs: 98 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 6.9 % / B_iso Wilson estimate: 24.6 Å² / R_merge(I) obs: 0.086 / R_sym value: 0.092 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.559 / Mean I/σ(I) obs: 2.9 / Num. unique all: 97586 / R_sym value: 0.607 / % possible all: 93.4

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz

Resolution: 1.8→28.5 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.94 / SU B: 5.435 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	5791	5 %	RANDOM
R_work	0.198	-	-	-
obs	0.199	109818	97.63 %	-
all	-	115798	-	-

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: 30.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.31 Å²	0 Å²	0 Å²
2-	-	-0.26 Å²	0 Å²
3-	-	-	-1.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→28.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7495	0	130	711	8336

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	7769
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.046	1.976	10571
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.509	5	969
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.251	25.462	368
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.008	15	1293
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.81	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1199
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5863
X-RAY DIFFRACTION	r_gen_planes_other
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	0.388	1.5	4816
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.738	2	7771
X-RAY DIFFRACTION	r_scbond_it	1.257	3	2953
X-RAY DIFFRACTION	r_scangle_it	2.076	4.5	2794
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→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	429	-
R_work	0.289	7515	-
obs	-	7515	91.64 %

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	3.5789	1.0462	0.9882	6.1007	-3.046	8.6835	-0.0925	0.0638	0.6426	0.883	0.3515	0.5381	-2.2065	-0.3773	-0.259	0.7471	0.0728	0.1232	0.0901	0.0613	0.2622	-24.808	31.492	0.908
2	1.5894	-3.043	1.0126	7.2874	-2.6754	8.2353	-0.0854	-0.0205	-0.2211	-0.2751	0.6477	1.2359	-0.8843	-1.3009	-0.5623	0.3866	-0.0396	-0.1079	0.5846	0.3895	0.5968	-32.891	23.177	-9.466
3	1.0686	0.3758	-0.0788	1.2441	0.0788	1.1729	-0.0274	0.1596	0.0425	-0.1617	-0.0216	0.0954	-0.0943	-0.1511	0.049	0.067	0.0307	-0.022	0.087	-0.0366	0.0341	-32.848	-1.489	7.922
4	0.8213	0.1539	0.891	2.6972	-3.0647	7.5454	-0.0282	0.3064	0.0752	-0.2072	0.2418	0.0086	-0.0923	0.2755	-0.2136	0.2245	-0.0669	0.0177	0.1486	0.0306	0.0908	-22.077	16.828	-4.475
5	3.1526	-1.8633	-1.8786	3.1355	1.7307	2.9497	-0.1954	0.0408	-0.5064	0.2803	-0.0684	0.328	0.2664	-0.0529	0.2638	0.0458	0.0114	0.0346	0.0669	-0.0431	0.1273	-13.957	-38.041	0.876
6	3.3843	-1.8671	-1.651	4.8573	2.1374	2.524	0.3192	0.318	0.0518	-0.6658	-0.203	-0.3901	-0.5138	0.0448	-0.1161	0.2442	0.054	0.0198	0.2336	-0.0207	0.1255	-10.829	-28.707	-10.538
7	0.9936	-0.1877	0.3904	1.5771	-0.049	1.2583	0.0188	0.1527	0.0199	-0.1633	-0.0372	-0.1537	-0.0459	0.2801	0.0184	0.0528	0.0119	0.0266	0.1053	-0.0045	0.0295	-9.519	-6.294	7.157
8	0.7123	0.7243	0.3898	0.9038	0.1452	4.5876	-0.0679	0.0621	0.0975	-0.1347	-0.0315	0.1728	-0.1798	-0.2713	0.0993	0.0777	0.0684	-0.0135	0.1109	-0.0344	0.1039	-22.302	-25.582	-4.001
9	3.0842	2.301	-2.0325	4.3013	-2.1283	3.7722	-0.1085	-0.0345	-0.5511	-0.2152	-0.1358	-0.4621	0.2437	-0.0886	0.2443	0.0587	-0.0412	0.0093	0.0576	0.03	0.1781	-31.63	-37.98	31.582
10	4.1851	3.9532	-2.0146	7.5986	-2.243	3.6155	0.5896	-0.4047	0.1827	0.8576	-0.5002	0.5329	-0.6501	-0.1138	-0.0894	0.2477	-0.1222	0.0496	0.2015	0.0005	0.0903	-36.431	-29.178	42.8
11	1.0284	-0.0796	0.2065	1.161	0.1893	1.0855	0.0279	-0.1083	0.002	0.1541	-0.0926	0.1176	-0.0605	-0.1808	0.0647	0.0733	-0.0118	0.0174	0.0695	-0.0382	0.0298	-32.444	-3.406	26.451
12	2.5033	1.5051	-0.6566	4.0516	-2.8112	5.374	0.397	-0.5381	-0.3055	0.5843	-0.5336	-0.4754	-0.3327	0.437	0.1366	0.1516	-0.1444	-0.0648	0.1632	0.0668	0.1125	-24.819	-25.123	37.195
13	2.0174	0.7301	0.5738	2.7745	1.1203	2.6686	-0.1173	0.1123	0.1983	-0.4493	-0.0012	0.0962	-0.3771	-0.0458	0.1185	0.0974	-0.0117	-0.0314	0.0573	0.0259	0.0706	-11.737	29.941	33.206
14	2.4567	0.7496	0.6692	3.1509	0.3623	3.4988	0.0604	0.0765	-0.0833	0.1928	0.0124	-0.4203	0.2691	0.441	-0.0728	0.0334	0.0167	-0.0263	0.1241	-0.0014	0.0917	-5.33	21.01	43.49
15	0.7531	-0.115	-0.1282	1.2187	0.1281	0.9805	0.021	-0.0644	-0.0084	0.132	-0.0248	-0.1436	0.006	0.2272	0.0038	0.0592	-0.0128	-0.0223	0.0762	0.0003	0.0231	-8.885	-4.51	26.134
16	0.6831	-0.2207	-0.3822	1.7265	1.3294	4.2775	-0.0454	-0.0427	-0.0553	0.0569	0.0069	0.0933	0.2606	-0.3337	0.0385	0.0556	-0.043	-0.0004	0.0649	-0.0115	0.0588	-16.32	15.808	38.651

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 69
2	X-RAY DIFFRACTION	2	A	70 - 104
3	X-RAY DIFFRACTION	3	A	105 - 210
4	X-RAY DIFFRACTION	4	A	211 - 240
5	X-RAY DIFFRACTION	5	B	0 - 69
6	X-RAY DIFFRACTION	6	B	70 - 104
7	X-RAY DIFFRACTION	7	B	105 - 210
8	X-RAY DIFFRACTION	8	B	211 - 240
9	X-RAY DIFFRACTION	9	C	0 - 69
10	X-RAY DIFFRACTION	10	C	70 - 104
11	X-RAY DIFFRACTION	11	C	105 - 210
12	X-RAY DIFFRACTION	12	C	211 - 240
13	X-RAY DIFFRACTION	13	D	0 - 69
14	X-RAY DIFFRACTION	14	D	70 - 104
15	X-RAY DIFFRACTION	15	D	105 - 210
16	X-RAY DIFFRACTION	16	D	211 - 240

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