PDB-6j9s: Penta mutant of Lactobacillus casei lactate dehydrogenase

ID or keywords:

Entry

Database: PDB / ID: 6j9s

Title

Penta mutant of Lactobacillus casei lactate dehydrogenase

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 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: 3VKU
Revision 1.0	Feb 6, 2019	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	6j9s.cif.gz	714.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6j9s_validation.pdf.gz	509.8 KB	Display	wwPDB validaton report
Full document	6j9s_full_validation.pdf.gz	526.4 KB	Display
Data in XML	6j9s_validation.xml.gz	67.7 KB	Display
Data in CIF	6j9s_validation.cif.gz	96 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9s ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9s	HTTPS FTP

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Related structure data

Related structure data	6j9tC 6j9uC 6jmlC 2zqzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2v6b-d 1hyh-d 6y91-d 4nd5-1 4nd5-2 6lym-d 6jml-1 6j9u-1 3pqd-1 4r7g-d 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

216 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
144 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
144 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	163.569, 82.893, 180.834
Angle α, β, γ (deg.)	90.00, 91.50, 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: SER / Beg label comp-ID: SER / 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	VAL	VAL	A	A	3 - 312	3 - 312
2	1	VAL	VAL	B	B	3 - 312	3 - 312
1	2	VAL	VAL	A	A	3 - 312	3 - 312
2	2	VAL	VAL	C	C	3 - 312	3 - 312
1	3	LYS	LYS	A	A	3 - 311	3 - 311
2	3	LYS	LYS	D	D	3 - 311	3 - 311
1	4	VAL	VAL	A	A	3 - 312	3 - 312
2	4	VAL	VAL	E	E	3 - 312	3 - 312
1	5	VAL	VAL	A	A	3 - 312	3 - 312
2	5	VAL	VAL	F	F	3 - 312	3 - 312
1	6	THR	THR	B	B	3 - 314	3 - 314
2	6	THR	THR	C	C	3 - 314	3 - 314
1	7	THR	THR	B	B	3 - 314	3 - 314
2	7	THR	THR	D	D	3 - 314	3 - 314
1	8	PHE	PHE	B	B	3 - 317	3 - 317
2	8	PHE	PHE	E	E	3 - 317	3 - 317
1	9	PHE	PHE	B	B	3 - 317	3 - 317
2	9	PHE	PHE	F	F	3 - 317	3 - 317
1	10	THR	THR	C	C	3 - 314	3 - 314
2	10	THR	THR	D	D	3 - 314	3 - 314
1	11	THR	THR	C	C	3 - 314	3 - 314
2	11	THR	THR	E	E	3 - 314	3 - 314
1	12	THR	THR	C	C	3 - 314	3 - 314
2	12	THR	THR	F	F	3 - 314	3 - 314
1	13	THR	THR	D	D	3 - 314	3 - 314
2	13	THR	THR	E	E	3 - 314	3 - 314
1	14	THR	THR	D	D	3 - 314	3 - 314
2	14	THR	THR	F	F	3 - 314	3 - 314
1	15	PHE	PHE	E	E	3 - 317	3 - 317
2	15	PHE	PHE	F	F	3 - 317	3 - 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.86 Å³/Da / Density % sol: 57.04 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 100mM sodium citrate, 200mM potassium sodium tartrate, 1.6M ammonium sulfate

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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: Jun 10, 2009
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→50 Å / Num. obs: 160457 / % possible obs: 97.1 % / Redundancy: 3.6 % / R_merge(I) obs: 0.046 / Net I/σ(I): 27.6
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.589 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8179 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZQZ

2zqz

Resolution: 2→41.07 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.94 / SU B: 8.409 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23417	7951	5 %	RANDOM
R_work	0.20873	-	-	-
obs	0.21	150558	96.96 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 50.146 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.36 Å²	-0 Å²	0.64 Å²
2-	-	2.41 Å²	0 Å²
3-	-	-	-3.78 Å²

Refinement step

Cycle: 1 / Resolution: 2→41.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14118	0	102	510	14730

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	14453
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	14125
X-RAY DIFFRACTION	r_angle_refined_deg	1.78	1.969	19581
X-RAY DIFFRACTION	r_angle_other_deg	1.609	3	32567
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.741	5	1826
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.154	25.49	592
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.108	15	2536
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.446	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	2285
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	16142
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	3007
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	18377	0.08
1	2	B	18377	0.08
2	1	A	18343	0.09
2	2	C	18343	0.09
3	1	A	18123	0.09
3	2	D	18123	0.09
4	1	A	18252	0.09
4	2	E	18252	0.09
5	1	A	18446	0.08
5	2	F	18446	0.08
6	1	B	18619	0.09
6	2	C	18619	0.09
7	1	B	18208	0.1
7	2	D	18208	0.1
8	1	B	19656	0.08
8	2	E	19656	0.08
9	1	B	19943	0.07
9	2	F	19943	0.07
10	1	C	18457	0.1
10	2	D	18457	0.1
11	1	C	18594	0.1
11	2	E	18594	0.1
12	1	C	18670	0.09
12	2	F	18670	0.09
13	1	D	18320	0.1
13	2	E	18320	0.1
14	1	D	18280	0.1
14	2	F	18280	0.1
15	1	E	19696	0.09
15	2	F	19696	0.09

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	649	-
R_work	0.281	11380	-
obs	-	-	99.81 %

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	1.5505	-0.0275	-0.4651	0.4237	-0.3066	1.7057	-0.0523	-0.3147	0.5308	-0.0334	0.0891	-0.0873	-0.1301	0.4861	-0.0367	0.078	-0.047	-0.0917	0.2353	-0.1094	0.4199	14.811	10.285	184.848
2	1.1949	-0.2058	-0.6517	0.4943	-0.0983	1.3467	-0.2884	0.2797	0.076	-0.0585	0.1518	-0.0226	0.2929	-0.1535	0.1366	0.1833	-0.1383	-0.0168	0.1756	0.0284	0.177	0.76	-8.447	160.109
3	0.9141	-0.0294	-0.1816	0.5227	0.1658	1.0473	0.1168	-0.2704	-0.167	-0.0134	-0.0398	-0.0096	0.4755	-0.1914	-0.0771	0.2826	-0.1584	-0.062	0.1684	0.0849	0.1447	37.521	-9.597	125.735
4	0.6602	0.1901	0.3508	0.785	-0.0281	1.3233	-0.0239	-0.0761	0.1424	-0.0482	-0.0064	-0.119	-0.0525	0.2186	0.0303	0.043	-0.0276	-0.0134	0.1301	-0.0209	0.2183	61.248	22.089	117.799
5	0.5326	0.0417	0.4609	0.3791	0.166	1.2415	0.0525	-0.1275	0.0512	-0.1621	-0.0803	0.0707	0.0815	-0.1923	0.0278	0.1494	-0.0165	-0.0557	0.0925	-0.0004	0.1974	31.653	12.555	100.435
6	0.3809	0.1804	0.2726	0.6787	0.3445	1.1313	0.0262	-0.377	0.1808	-0.0063	-0.1515	0.0629	0.0495	-0.396	0.1253	0.0071	-0.0433	-0.0032	0.4455	-0.1217	0.1738	36.578	22.606	141.355

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 312
2	X-RAY DIFFRACTION	1	A	401 - 402
3	X-RAY DIFFRACTION	2	B	3 - 317
4	X-RAY DIFFRACTION	2	B	401 - 404
5	X-RAY DIFFRACTION	3	C	3 - 314
6	X-RAY DIFFRACTION	3	C	401 - 403
7	X-RAY DIFFRACTION	4	D	3 - 314
8	X-RAY DIFFRACTION	4	D	401 - 403
9	X-RAY DIFFRACTION	5	E	3 - 317
10	X-RAY DIFFRACTION	5	E	401 - 404
11	X-RAY DIFFRACTION	6	F	3 - 317
12	X-RAY DIFFRACTION	6	F	401 - 403

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