PDB-6j9u: Complex structure of Lactobacillus casei lactate dehydrogenase pe...

ID or keywords:

Entry

Database: PDB / ID: 6j9u

Title

Complex structure of Lactobacillus casei lactate dehydrogenase penta mutant with pyruvate

Components

L-lactate dehydrogenase

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

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

Biological species

Lactobacillus casei subsp. casei ATCC 393 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 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	Jan 24, 2019	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Feb 6, 2019	ID: 3VPF
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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
Revision 2.1	Nov 22, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6j9u.cif.gz	707.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6j9u_validation.pdf.gz	509.9 KB	Display	wwPDB validaton report
Full document	6j9u_full_validation.pdf.gz	531.5 KB	Display
Data in XML	6j9u_validation.xml.gz	62.4 KB	Display
Data in CIF	6j9u_validation.cif.gz	85.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9u ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9u	HTTPS FTP

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Related structure data

Related structure data	6j9sC 6j9tC 6jmlC 2zqzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6jml-1 6j9t-1 6jml-2 3pqd-2 6vdi-1 1uxk-1 6j9t-2 2zqz-1 4lmr-1 1ur5-1 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 (11) #154 - Oct 2012 Citric Acid Cycle similarity (6) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #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)	165.320, 82.800, 180.150
Angle α, β, γ (deg.)	90.00, 91.52, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ILE	ILE	THR	THR	A	A	4 - 314	4 - 314
2	1	ILE	ILE	THR	THR	B	B	4 - 314	4 - 314
1	2	ILE	ILE	THR	THR	A	A	4 - 314	4 - 314
2	2	ILE	ILE	THR	THR	C	C	4 - 314	4 - 314
1	3	ILE	ILE	THR	THR	A	A	4 - 314	4 - 314
2	3	ILE	ILE	THR	THR	D	D	4 - 314	4 - 314
1	4	ILE	ILE	THR	THR	A	A	4 - 314	4 - 314
2	4	ILE	ILE	THR	THR	E	E	4 - 314	4 - 314
1	5	ILE	ILE	THR	THR	A	A	4 - 314	4 - 314
2	5	ILE	ILE	THR	THR	F	F	4 - 314	4 - 314
1	6	SER	SER	PHE	PHE	B	B	3 - 317	3 - 317
2	6	SER	SER	PHE	PHE	C	C	3 - 317	3 - 317
1	7	SER	SER	PHE	PHE	B	B	3 - 317	3 - 317
2	7	SER	SER	PHE	PHE	D	D	3 - 317	3 - 317
1	8	ILE	ILE	ALA	ALA	B	B	4 - 316	4 - 316
2	8	ILE	ILE	ALA	ALA	E	E	4 - 316	4 - 316
1	9	SER	SER	ALA	ALA	B	B	3 - 316	3 - 316
2	9	SER	SER	ALA	ALA	F	F	3 - 316	3 - 316
1	10	SER	SER	PHE	PHE	C	C	3 - 317	3 - 317
2	10	SER	SER	PHE	PHE	D	D	3 - 317	3 - 317
1	11	ILE	ILE	ALA	ALA	C	C	4 - 316	4 - 316
2	11	ILE	ILE	ALA	ALA	E	E	4 - 316	4 - 316
1	12	SER	SER	ALA	ALA	C	C	3 - 316	3 - 316
2	12	SER	SER	ALA	ALA	F	F	3 - 316	3 - 316
1	13	ILE	ILE	ALA	ALA	D	D	4 - 316	4 - 316
2	13	ILE	ILE	ALA	ALA	E	E	4 - 316	4 - 316
1	14	SER	SER	ALA	ALA	D	D	3 - 316	3 - 316
2	14	SER	SER	ALA	ALA	F	F	3 - 316	3 - 316
1	15	ILE	ILE	PHE	PHE	E	E	4 - 317	4 - 317
2	15	ILE	ILE	PHE	PHE	F	F	4 - 317	4 - 317

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: 35670.648 Da / Num. of mol.: 6 / Mutation: S55E, N56D, E164K, D223N, A224K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei subsp. casei ATCC 393 (bacteria) Gene: ldh, LBCZ_2323 / Production host: Escherichia coli (E. coli) / References: UniProt: S6C1Z0, L-lactate dehydrogenase
#2: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₄O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.88 Å³/Da / Density % sol: 57.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM sodium citrate, 200mM potassium sodium tartrate, 1.6M ammonium sulfate, 10mM sodium pyruvate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2012
Radiation	Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.79→50 Å / Num. obs: 58891 / % possible obs: 97.5 % / Redundancy: 5.4 % / R_merge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.79→2.95 Å / R_merge(I) obs: 0.581 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8449 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
iMOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZQZ

2zqz

Resolution: 2.79→46.9 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.918 / SU B: 27.288 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R Free: 0.333 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22667	2998	5.1 %	RANDOM
R_work	0.1912	-	-	-
obs	0.19302	55893	97.03 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 48.374 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.57 Å²	-0 Å²	0.26 Å²
2-	-	-0.18 Å²	-0 Å²
3-	-	-	-0.39 Å²

Refinement step

Cycle: 1 / Resolution: 2.79→46.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14468	0	63	65	14596

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	14780
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	14440
X-RAY DIFFRACTION	r_angle_refined_deg	1.569	1.968	20039
X-RAY DIFFRACTION	r_angle_other_deg	1.385	3	33297
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.748	5	1875
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.181	25.477	608
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.186	15	2592
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.579	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2330
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	16595
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	3081
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	18861	0.1
1	2	B	18861	0.1
2	1	A	19177	0.09
2	2	C	19177	0.09
3	1	A	18954	0.1
3	2	D	18954	0.1
4	1	A	18860	0.1
4	2	E	18860	0.1
5	1	A	18899	0.09
5	2	F	18899	0.09
6	1	B	19215	0.1
6	2	C	19215	0.1
7	1	B	18984	0.11
7	2	D	18984	0.11
8	1	B	19670	0.08
8	2	E	19670	0.08
9	1	B	19804	0.07
9	2	F	19804	0.07
10	1	C	19488	0.1
10	2	D	19488	0.1
11	1	C	19158	0.1
11	2	E	19158	0.1
12	1	C	19218	0.1
12	2	F	19218	0.1
13	1	D	18865	0.12
13	2	E	18865	0.12
14	1	D	18936	0.11
14	2	F	18936	0.11
15	1	E	19635	0.09
15	2	F	19635	0.09

LS refinement shell

Resolution: 2.794→2.866 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.338	212	-
R_work	0.286	4046	-
obs	-	-	95 %

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	0.5978	-0.0602	-0.4322	0.1144	-0.102	1.0628	0.0545	-0.211	0.2548	-0.0611	0.047	0.0108	-0.0622	0.293	-0.1016	0.0549	-0.0601	-0.0265	0.1416	-0.0649	0.2301	15.605	10.526	183.686
2	0.5468	-0.2079	-0.3952	0.2306	-0.0735	0.8618	-0.1201	0.0776	0.0588	-0.0306	0.062	-0.0214	0.1884	-0.101	0.0581	0.0901	-0.0803	-0.0128	0.1078	0.0249	0.1184	0.623	-8.535	159.601
3	0.3452	-0.1007	-0.0499	0.1337	0.086	0.5077	0.1005	-0.1307	-0.0184	-0.0345	-0.0388	-0.0388	0.24	-0.1415	-0.0616	0.1918	-0.1016	-0.0451	0.1329	0.0521	0.0893	37.392	-10.237	124.863
4	0.2659	0.1142	0.2468	0.4322	-0.0928	0.6385	-0.0142	-0.0371	0.0365	-0.0173	-0.0236	-0.0212	-0.0159	0.0705	0.0379	0.0527	-0.0017	-0.0273	0.0641	0.0015	0.1596	62.192	22.801	117.895
5	0.1941	0.0863	0.1852	0.1555	0.1721	0.6148	0.0175	-0.1029	0.0424	-0.0838	-0.0644	0.0082	0.0109	-0.0862	0.0469	0.0971	0.0092	-0.029	0.0606	-0.0135	0.1683	32.033	12.652	99.874
6	0.0817	0.0944	0.1616	0.3286	0.1021	0.5209	0.0015	-0.1293	0.0422	-0.0419	-0.0954	-0.0324	0.033	-0.2299	0.0939	0.0152	-0.0224	0.0013	0.2602	-0.0599	0.0955	36.797	22.569	140.894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 314
2	X-RAY DIFFRACTION	1	A	401 - 402
3	X-RAY DIFFRACTION	2	B	3 - 317
4	X-RAY DIFFRACTION	2	B	401 - 402
5	X-RAY DIFFRACTION	3	C	3 - 317
6	X-RAY DIFFRACTION	3	C	401 - 402
7	X-RAY DIFFRACTION	4	D	3 - 317
8	X-RAY DIFFRACTION	4	D	401 - 402
9	X-RAY DIFFRACTION	5	E	4 - 318
10	X-RAY DIFFRACTION	5	E	401 - 402
11	X-RAY DIFFRACTION	6	F	3 - 318
12	X-RAY DIFFRACTION	6	F	401 - 402

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