PDB-6jml: Re-refined structure of R-state L-lactate dehydrogenase fromLacto...

ID or keywords:

Entry

Database: PDB / ID: 6jml

Title

Re-refined structure of R-state L-lactate dehydrogenase fromLactobacillus casei

Components

L-lactate dehydrogenase

Keywords

OXIDOREDUCTASE / ROSSMANN FOLD / GLYCOLYSIS

Function / homology

Function and homology information

L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / cytoplasm
Similarity search - Function

Biological species

Lactobacillus casei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Arai, K. / Miyanaga, A. / Uchikoba, H. / Fushinobu, S. / Taguchi, H.

Citation

Journal: To Be Published
Title: Crystal structure of penta mutant of L-lactate dehydrogenase from Lactobacillus casei
Authors: Arai, K. / Miyanaga, A. / Uchikoba, H. / Fushinobu, S. / Taguchi, H.

History

Deposition	Mar 12, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 6, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6jml.cif.gz	713.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6jml.ent.gz	597.3 KB	Display	PDB format
PDBx/mmJSON format	6jml.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	6j9sC 6j9tC 6j9uC 2zqzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6j9s-2 6j9t-1 6j9u-1 2zqz-1 6j9u-2 1u5a-1 7by8-d 6jt9-d 6bb1-2 5hs4-1 Search similar-shape structures by Omokage search (details) 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (10)

Deposited unit

A: L-lactate dehydrogenase

B: L-lactate dehydrogenase

C: L-lactate dehydrogenase

D: L-lactate dehydrogenase

E: L-lactate dehydrogenase

F: L-lactate dehydrogenase

hetero molecules

215 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-lactate dehydrogenase

B: L-lactate dehydrogenase

hetero molecules

A: L-lactate dehydrogenase

B: L-lactate dehydrogenase

hetero molecules

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

2

C: L-lactate dehydrogenase

D: L-lactate dehydrogenase

E: L-lactate dehydrogenase

F: L-lactate dehydrogenase

hetero molecules

defined by author&software
143 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	164.382, 82.893, 179.771
Angle α, β, γ (deg.)	90.00, 91.21, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	A	A	4 - 317	4 - 317
2	1	PHE	PHE	B	B	4 - 317	4 - 317
1	2	LEU	LEU	A	A	4 - 313	4 - 313
2	2	LEU	LEU	C	C	4 - 313	4 - 313
1	3	ALA	ALA	A	A	4 - 316	4 - 316
2	3	ALA	ALA	D	D	4 - 316	4 - 316
1	4	PHE	PHE	A	A	4 - 317	4 - 317
2	4	PHE	PHE	E	E	4 - 317	4 - 317
1	5	PHE	PHE	A	A	4 - 317	4 - 317
2	5	PHE	PHE	F	F	4 - 317	4 - 317
1	6	LEU	LEU	B	B	4 - 313	4 - 313
2	6	LEU	LEU	C	C	4 - 313	4 - 313
1	7	ALA	ALA	B	B	4 - 316	4 - 316
2	7	ALA	ALA	D	D	4 - 316	4 - 316
1	8	ALA	ALA	B	B	4 - 316	4 - 316
2	8	ALA	ALA	E	E	4 - 316	4 - 316
1	9	ALA	ALA	B	B	4 - 318	4 - 318
2	9	ALA	ALA	F	F	4 - 318	4 - 318
1	10	LEU	LEU	C	C	4 - 313	4 - 313
2	10	LEU	LEU	D	D	4 - 313	4 - 313
1	11	LEU	LEU	C	C	4 - 313	4 - 313
2	11	LEU	LEU	E	E	4 - 313	4 - 313
1	12	LEU	LEU	C	C	4 - 313	4 - 313
2	12	LEU	LEU	F	F	4 - 313	4 - 313
1	13	ALA	ALA	D	D	4 - 316	4 - 316
2	13	ALA	ALA	E	E	4 - 316	4 - 316
1	14	ALA	ALA	D	D	4 - 316	4 - 316
2	14	ALA	ALA	F	F	4 - 316	4 - 316
1	15	ALA	ALA	E	E	4 - 316	4 - 316
2	15	ALA	ALA	F	F	4 - 316	4 - 316

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	L-lactate dehydrogenase / L-LDH Mass: 35570.449 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: ldh / Plasmid: PLCEX / Production host: Escherichia coli (E. coli) / Strain (production host): MV1184 / References: UniProt: P00343, L-lactate dehydrogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.93 Å³/Da / Density % sol: 58.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: ammonium sulfate, sodium citrate, potassium sodium tartrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2000
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.1→34.1 Å / Num. obs: 168255 / % possible obs: 99.9 % / Redundancy: 2.6 % / B_iso Wilson estimate: 36.9 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 7.1
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.509 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7480 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZQZ

2zqz

Resolution: 2.3→34.1 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.937 / SU B: 14.79 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22166	5411	5 %	RANDOM
R_work	0.19396	-	-	-
obs	0.19535	102055	99.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 48.718 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.93 Å²	0 Å²	0.48 Å²
2-	-	0.83 Å²	0 Å²
3-	-	-	0.08 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→34.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14212	0	60	263	14535

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	14513
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	13788
X-RAY DIFFRACTION	r_angle_refined_deg	1.747	1.629	19692
X-RAY DIFFRACTION	r_angle_other_deg	1.429	1.58	32011
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.472	5	1843
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.293	24.343	647
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.729	15	2511
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.715	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1992
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	16080
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2745
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	1.952	2.493	7402
X-RAY DIFFRACTION	r_mcbond_other	1.95	2.493	7401
X-RAY DIFFRACTION	r_mcangle_it	2.902	3.728	9235
X-RAY DIFFRACTION	r_mcangle_other	2.902	3.728	9236
X-RAY DIFFRACTION	r_scbond_it	2.543	2.809	7111
X-RAY DIFFRACTION	r_scbond_other	2.541	2.809	7104
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.927	4.083	10446
X-RAY DIFFRACTION	r_long_range_B_refined	5.072	29.761	16053
X-RAY DIFFRACTION	r_long_range_B_other	5.066	29.755	16044
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	10068	0.05
1	2	B	10068	0.05
2	1	A	9669	0.05
2	2	C	9669	0.05
3	1	A	9895	0.05
3	2	D	9895	0.05
4	1	A	10045	0.05
4	2	E	10045	0.05
5	1	A	10100	0.05
5	2	F	10100	0.05
6	1	B	9613	0.06
6	2	C	9613	0.06
7	1	B	9835	0.05
7	2	D	9835	0.05
8	1	B	10164	0.06
8	2	E	10164	0.06
9	1	B	10285	0.05
9	2	F	10285	0.05
10	1	C	9459	0.06
10	2	D	9459	0.06
11	1	C	9620	0.06
11	2	E	9620	0.06
12	1	C	9632	0.06
12	2	F	9632	0.06
13	1	D	9817	0.06
13	2	E	9817	0.06
14	1	D	9846	0.05
14	2	F	9846	0.05
15	1	E	10162	0.06
15	2	F	10162	0.06

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	386	-
R_work	0.264	7493	-
obs	-	-	99.99 %

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	1.0725	0.0107	-0.5365	0.3228	-0.1976	1.2629	-0.0625	-0.2638	0.2847	-0.0273	0.07	-0.0518	-0.0661	0.3676	-0.0076	0.2632	-0.0218	-0.0321	0.2044	-0.0599	0.1231	20.576	10.832	3.671
2	1.1968	-0.2514	-0.6799	0.5241	-0.2624	1.4963	-0.3078	0.2286	-0.0369	-0.091	0.1035	-0.0616	0.3571	-0.1676	0.2043	0.4227	-0.1391	0.0703	0.1688	-0.0176	0.0344	5.351	-8.75	-20.495
3	0.8646	-0.1248	-0.3533	0.4489	0.2694	1.271	0.0141	-0.1123	-0.0594	0.0733	0.0312	0.0159	0.503	-0.1481	-0.0453	0.4975	-0.0971	-0.0286	0.1836	0.0473	0.0144	38.259	-9.523	125.068
4	0.6689	-0.0123	0.3538	1.0268	0.0815	1.4035	0.0258	-0.0324	0.2093	-0.1054	0.0992	-0.2379	-0.0458	0.3291	-0.125	0.202	-0.0278	0.0645	0.2175	-0.0687	0.1654	62.913	22.281	117.43
5	0.4993	-0.1207	0.2859	0.6316	0.239	1.3633	0.0993	-0.0283	0.0991	-0.1719	-0.0742	0.0532	0.088	-0.1895	-0.0251	0.3034	0.0018	-0.0223	0.195	0.047	0.0578	32.227	12.782	99.854
6	0.6814	0.0872	0.2684	0.6386	0.3706	1.3849	0.0276	-0.3298	0.2486	0.0448	-0.0557	0.0182	0.0894	-0.2839	0.0281	0.2018	-0.0133	0.0399	0.3687	-0.1133	0.1004	37.45	22.603	140.849

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 317
2	X-RAY DIFFRACTION	1	A	401 - 402
3	X-RAY DIFFRACTION	1	A	501 - 544
4	X-RAY DIFFRACTION	1	B	548
5	X-RAY DIFFRACTION	2	B	4 - 318
6	X-RAY DIFFRACTION	2	B	401 - 402
7	X-RAY DIFFRACTION	3	C	4 - 313
8	X-RAY DIFFRACTION	3	C	401 - 402
9	X-RAY DIFFRACTION	3	C	501 - 539
10	X-RAY DIFFRACTION	3	D	532
11	X-RAY DIFFRACTION	3	E	529 - 545
12	X-RAY DIFFRACTION	3	F	540
13	X-RAY DIFFRACTION	4	D	4 - 316
14	X-RAY DIFFRACTION	4	D	401 - 402
15	X-RAY DIFFRACTION	4	F	511
16	X-RAY DIFFRACTION	5	E	4 - 317
17	X-RAY DIFFRACTION	5	E	401 - 402
18	X-RAY DIFFRACTION	5	F	517
19	X-RAY DIFFRACTION	6	F	4 - 318
20	X-RAY DIFFRACTION	6	F	401 - 402
21	X-RAY DIFFRACTION	6	D	536

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