PDB-3p7m: Structure of putative lactate dehydrogenase from Francisella tula...

ID or keywords:

Entry

Database: PDB / ID: 3p7m

Title

Structure of putative lactate dehydrogenase from Francisella tularensis subsp. tularensis SCHU S4

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE /

putative dehydrogenase /

enzyme /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process /

tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function

Biological species

Francisella tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Osinski, T. / Cymborowski, M. / Zimmerman, M.D. / Gordon, E. / Grimshaw, S. / Skarina, T. / Chruszcz, M. / Savchenko, A. / Anderson, W. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Structure of putative lactate dehydrogenase from Francisella tularensis subsp. tularensis SCHU S4
Authors: Osinski, T. / Cymborowski, M. / Zimmerman, M.D. / Gordon, E. / Grimshaw, S. / Skarina, T. / Chruszcz, M. / Savchenko, A. / Anderson, W. / Minor, W.

History

Deposition	Oct 12, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 20, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3p7m.cif.gz	479.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3p7m.ent.gz	399.1 KB	Display	PDB format
PDBx/mmJSON format	3p7m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p7/3p7m ftp://data.pdbj.org/pub/pdb/validation_reports/p7/3p7m	HTTPS FTP

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Related structure data

Related structure data	3gvhS S: Starting model for refinement
Similar structure data	4lmr-1 6j9u-2 1pze-1 6vdi-1 3gvi-2 3pqd-2 6j9u-1 6j9t-1 6jml-2 4b7u-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: IDP02372

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (7) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

C: Malate dehydrogenase

D: Malate dehydrogenase

hetero molecules

140 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)	78.740, 99.147, 83.345
Angle α, β, γ (deg.)	90.00, 103.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	B
2	2	D

/ NCS ensembles :

ID
1
2

#1: Protein	Malate dehydrogenase / Mass: 34924.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Strain: tularensis / Gene: FTT_0535c, mdh / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8G942, malate dehydrogenase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 538 / 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: 45.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M NH4 dihydrogen Phosphate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2009 / Details: mirrors
Radiation	Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 62128 / Num. obs: 62128 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 31.2 Å² / R_merge(I) obs: 0.126 / R_sym value: 0.126 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.497 / Mean I/σ(I) obs: 2.73 / Num. unique all: 3136 / R_sym value: 0.497 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-3000		phasing
MOLREP		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 3GVH

3gvh

Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.926 / SU B: 11.32 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23307	2964	5.1 %	RANDOM
R_work	0.18204	-	-	-
all	0.18468	54811	-	-
obs	0.18468	54811	91.39 %	-

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: 27.599 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	0 Å²	-0.72 Å²
2-	-	-0.33 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9367	0	10	538	9915

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	9563
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	6302
X-RAY DIFFRACTION	r_angle_refined_deg	1.6	1.986	12947
X-RAY DIFFRACTION	r_angle_other_deg	4.332	3	15604
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.228	5	1284
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.447	25.912	362
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.008	15	1705
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.646	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1552
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	10711
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	1670
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	0.66	1.5	6322
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	2632
X-RAY DIFFRACTION	r_mcangle_it	1.157	2	10135
X-RAY DIFFRACTION	r_scbond_it	2.896	3	3241
X-RAY DIFFRACTION	r_scangle_it	3.942	4.5	2809
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1854	tight positional	0.07	0.05
2	2	B	1840	tight positional	0.06	0.05
1	1	C	2013	loose positional	0.16	5
2	2	D	1931	loose positional	0.15	5
1	1	A	1854	tight thermal	0.19	0.5
2	2	B	1840	tight thermal	0.19	0.5
1	1	C	2013	loose thermal	0.79	10
2	2	D	1931	loose thermal	0.45	10

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.259	195	-
R_work	0.2	3334	-
obs	-	-	76.15 %

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	0.1245	-0.2004	0.357	0.902	0.1345	2.7719	0.0502	-0.0124	0.0227	-0.0299	-0.0304	0.0515	0.1734	-0.2335	-0.0199	0.0475	-0.0227	0.0205	0.0375	0.0094	0.0385	-4.82	-5.452	17.011
2	1.8121	0.965	1.761	1.8646	0.7615	4.3446	0.0013	-0.1077	0.0254	0.0262	0.0205	0.1527	0.041	-0.3903	-0.0218	0.031	-0.0003	0.0305	0.0399	0.0115	0.0384	-9.085	-1.334	14.51
3	28.488	-17.4114	36.0416	24.2802	-22.7602	31.7534	0.604	-2.0575	-2.5361	-2.4283	0.7768	-1.6682	1.3843	-2.4246	-1.3808	0.8463	-0.0776	0.0438	0.3477	-0.1359	0.914	-8.897	-20.87	-6.929
4	2.4828	0.9105	-0.0971	1.7412	-0.5251	2.2948	-0.059	0.1954	-0.0711	-0.3379	0.0553	0.1539	0.2189	-0.4146	0.0036	0.1193	-0.0087	-0.0432	0.1334	-0.0072	0.0545	-10.878	-1.164	-1.808
5	0.8172	0.1257	0.1948	0.9254	0.3696	1.0456	-0.0506	0.2004	-0.0622	-0.1557	0.0742	-0.0165	-0.0432	0.0406	-0.0236	0.1063	-0.0477	0.0164	0.062	-0.0183	0.0072	9.797	-3.679	-5.732
6	1.0983	0.3983	-0.1898	1.9505	-0.3464	2.148	0.004	0.0727	-0.0808	-0.0376	0.0561	-0.116	0.21	0.0773	-0.0601	0.0681	0.0002	0.0102	0.0101	-0.0152	0.027	13.625	-17.194	14.148
7	1.0931	1.7188	-0.2307	3.0142	0.1307	2.1833	0.0335	-0.0152	-0.1676	-0.0051	-0.0575	-0.142	0.1757	-0.1392	0.024	0.1625	0.0093	-0.051	0.0146	0.0073	0.0958	10.066	-31.238	24.566
8	0.711	-0.1853	0.4491	1.2542	0.2865	0.425	0.0664	-0.1786	0.0154	0.1427	-0.1023	0.1059	0.1092	-0.1813	0.0359	0.1243	-0.0662	0.0311	0.0914	0.002	0.0363	-2.58	-13.29	37.578
9	1.0415	-0.8352	0.4047	0.6643	-0.2617	1.4268	0.0621	-0.0492	-0.0687	0.0155	0.0227	0.0487	0.2519	-0.1445	-0.0848	0.1716	-0.0491	-0.0186	0.0259	0.0265	0.0418	7.814	-18.593	34.184
10	0.6659	0.746	-0.025	2.3651	-0.1401	1.4064	0.1279	-0.2575	-0.0791	0.3804	-0.1383	0.0157	0.0496	-0.0426	0.0104	0.1682	-0.0329	-0.0039	0.1084	0.0426	0.0296	4.454	-25.524	43.741
11	2.312	-0.2401	-0.3723	0.9773	0.4017	1.3793	-0.0117	-0.0109	-0.0315	0.0768	0.0155	-0.1139	-0.0221	0.1777	-0.0038	0.0643	0.0077	-0.0263	0.0346	-0.0147	0.0445	31.676	5.391	30.739
12	2.9159	1.8451	-0.9277	1.2624	-0.0733	2.2537	-0.0621	0.0689	-0.0618	-0.0534	0.17	-0.0812	0.0013	0.4902	-0.1079	0.0203	0.0049	-0.0027	0.1532	-0.0739	0.1011	45.166	5.374	23.744
13	2.0461	-0.4934	0.7004	0.7407	0.0121	0.6876	-0.1627	0.0531	-0.0304	-0.0063	0.161	-0.0734	-0.1362	0.1083	0.0017	0.0739	-0.0489	0.0376	0.0681	-0.0362	0.0394	32.553	7.656	11.141
14	3.9876	1.1978	2.5357	1.606	-0.2361	2.5683	-0.1683	0.242	0.1703	-0.2011	0.1005	-0.0227	-0.0985	0.2508	0.0677	0.1429	-0.0771	0.0649	0.1167	-0.0386	0.0496	27.385	12.773	-3.508
15	1.2444	-0.1376	0.0456	0.1031	-0.1213	0.497	-0.0541	0.1703	-0.0412	-0.0483	0.0451	-0.0789	-0.0652	0.1883	0.009	0.0781	-0.1122	0.0664	0.2057	-0.0953	0.0776	38.089	7.297	8.593
16	1.346	-0.2652	-0.0713	0.8149	0.4389	2.2902	0.0256	0.0406	0.0945	-0.0435	0.0362	0.0011	-0.1205	0.0095	-0.0617	0.0641	-0.011	0.022	0.007	-0.0018	0.0267	16.046	18.203	20.142
17	2.459	-0.0529	-1.6356	2.8106	0.1725	4.5308	0.0722	-0.2557	0.4918	0.2808	0.0469	-0.09	-0.4352	0.3397	-0.1191	0.1408	0.0004	0.0079	0.0408	-0.031	0.1233	10.018	28.355	30.767
18	1.4028	-0.9593	0.2614	1.5088	-0.4297	0.6716	0.0218	-0.152	0.125	0.1218	0.0245	0.0015	-0.0523	-0.0245	-0.0462	0.0871	-0.0271	0.0211	0.0481	-0.0322	0.028	8.868	11.35	42.822
19	5.4484	5.0383	7.2423	9.8974	5.1703	9.5214	0.4364	-0.2651	-0.2441	0.5908	-0.2346	-0.3997	0.4947	-0.3059	-0.2018	0.1274	-0.0271	0.0075	0.0944	0.0582	0.058	12.858	-4.669	54.833
20	0.5728	0.0115	0.2339	0.8517	-0.1567	0.8178	0.0701	-0.0879	0.1572	0.197	-0.0254	0.0871	-0.1836	-0.1028	-0.0447	0.1356	-0.0005	0.0559	0.0359	-0.0303	0.0743	6.037	16.21	43.887

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 53
2	X-RAY DIFFRACTION	2	A	54 - 81
3	X-RAY DIFFRACTION	3	A	82 - 89
4	X-RAY DIFFRACTION	4	A	90 - 139
5	X-RAY DIFFRACTION	5	A	140 - 318
6	X-RAY DIFFRACTION	6	B	1 - 62
7	X-RAY DIFFRACTION	7	B	63 - 124
8	X-RAY DIFFRACTION	8	B	125 - 225
9	X-RAY DIFFRACTION	9	B	226 - 270
10	X-RAY DIFFRACTION	10	B	271 - 317
11	X-RAY DIFFRACTION	11	C	2 - 90
12	X-RAY DIFFRACTION	12	C	91 - 124
13	X-RAY DIFFRACTION	13	C	125 - 168
14	X-RAY DIFFRACTION	14	C	169 - 207
15	X-RAY DIFFRACTION	15	C	208 - 318
16	X-RAY DIFFRACTION	16	D	1 - 57
17	X-RAY DIFFRACTION	17	D	58 - 124
18	X-RAY DIFFRACTION	18	D	125 - 188
19	X-RAY DIFFRACTION	19	D	189 - 209
20	X-RAY DIFFRACTION	20	D	210 - 318

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