PDB-6j9t: Complex structure of Lactobacillus casei lactate dehydrogenase wi...

ID or keywords:

Entry

Database: PDB / ID: 6j9t

Title

Complex structure of Lactobacillus casei lactate dehydrogenase with fructose-1,6-bisphosphate

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: 2.7 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: 3VKV
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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	6j9t.cif.gz	708.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6j9t_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6j9t_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6j9t_validation.xml.gz	63.3 KB	Display
Data in CIF	6j9t_validation.cif.gz	86.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9t ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9t	HTTPS FTP

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Related structure data

Related structure data	6j9sC 6j9uC 6jmlC 2zqzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2zqz-1 6jml-2 6jml-1 6j9u-2 6j9u-1 2zqz-2 1pze-1 6vdh-1 6vdi-1 4lmr-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) #50 - Feb 2004 Glycolytic Enzymes 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)	164.250, 83.582, 180.094
Angle α, β, γ (deg.)	90.00, 91.53, 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	SER	SER	ALA	ALA	A	A	3 - 316	3 - 316
2	1	SER	SER	ALA	ALA	B	B	3 - 316	3 - 316
1	2	SER	SER	ASP	ASP	A	A	3 - 315	3 - 315
2	2	SER	SER	ASP	ASP	C	C	3 - 315	3 - 315
1	3	ILE	ILE	ALA	ALA	A	A	4 - 316	4 - 316
2	3	ILE	ILE	ALA	ALA	D	D	4 - 316	4 - 316
1	4	ILE	ILE	ALA	ALA	A	A	4 - 316	4 - 316
2	4	ILE	ILE	ALA	ALA	E	E	4 - 316	4 - 316
1	5	SER	SER	ALA	ALA	A	A	3 - 316	3 - 316
2	5	SER	SER	ALA	ALA	F	F	3 - 316	3 - 316
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	ILE	ILE	ALA	ALA	B	B	4 - 316	4 - 316
2	7	ILE	ILE	ALA	ALA	D	D	4 - 316	4 - 316
1	8	ILE	ILE	PHE	PHE	B	B	4 - 317	4 - 317
2	8	ILE	ILE	PHE	PHE	E	E	4 - 317	4 - 317
1	9	SER	SER	ALA	ALA	B	B	3 - 318	3 - 318
2	9	SER	SER	ALA	ALA	F	F	3 - 318	3 - 318
1	10	ILE	ILE	PHE	PHE	C	C	4 - 317	4 - 317
2	10	ILE	ILE	PHE	PHE	D	D	4 - 317	4 - 317
1	11	ILE	ILE	PHE	PHE	C	C	4 - 317	4 - 317
2	11	ILE	ILE	PHE	PHE	E	E	4 - 317	4 - 317
1	12	SER	SER	PHE	PHE	C	C	3 - 317	3 - 317
2	12	SER	SER	PHE	PHE	F	F	3 - 317	3 - 317
1	13	ILE	ILE	PHE	PHE	D	D	4 - 317	4 - 317
2	13	ILE	ILE	PHE	PHE	E	E	4 - 317	4 - 317
1	14	ILE	ILE	ALA	ALA	D	D	4 - 316	4 - 316
2	14	ILE	ILE	ALA	ALA	F	F	4 - 316	4 - 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: 35570.449 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: SO₄

#3: Sugar

ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₄O₁₂P₂

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.9 Å³/Da / Density % sol: 57.51 %
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, 2mM fructose-1,6-bisphosphate

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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: 2.7→50 Å / Num. obs: 67283 / % possible obs: 99.9 % / Redundancy: 7.4 % / R_merge(I) obs: 0.076 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.7→2.85 Å / R_merge(I) obs: 0.367 / Mean I/σ(I) obs: 2 / Num. unique obs: 9734 / % possible all: 99.6

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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: 2.7→41.18 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.919 / SU B: 21.348 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.869 / ESU R Free: 0.297 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2262	3405	5.1 %	RANDOM
R_work	0.19556	-	-	-
obs	0.19712	63871	99.91 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 47.735 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.17 Å²	-0 Å²	0.15 Å²
2-	-	0.15 Å²	-0 Å²
3-	-	-	-0.32 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→41.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14375	0	90	110	14575

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	14715
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	14288
X-RAY DIFFRACTION	r_angle_refined_deg	1.568	1.97	19981
X-RAY DIFFRACTION	r_angle_other_deg	1.28	3	32938
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.77	5	1866
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.125	25.486	607
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.728	15	2538
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.279	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	2332
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	16518
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	3072
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	19472	0.06
1	2	B	19472	0.06
2	1	A	19312	0.07
2	2	C	19312	0.07
3	1	A	19256	0.08
3	2	D	19256	0.08
4	1	A	18961	0.07
4	2	E	18961	0.07
5	1	A	19501	0.06
5	2	F	19501	0.06
6	1	B	19457	0.07
6	2	C	19457	0.07
7	1	B	19254	0.08
7	2	D	19254	0.08
8	1	B	19137	0.07
8	2	E	19137	0.07
9	1	B	19763	0.07
9	2	F	19763	0.07
10	1	C	19297	0.08
10	2	D	19297	0.08
11	1	C	18983	0.07
11	2	E	18983	0.07
12	1	C	19448	0.07
12	2	F	19448	0.07
13	1	D	19170	0.08
13	2	E	19170	0.08
14	1	D	19371	0.08
14	2	F	19371	0.08
15	1	E	19256	0.06
15	2	F	19256	0.06

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.348	262	-
R_work	0.279	4664	-
obs	-	-	99.98 %

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	0.8909	0.0471	-0.4872	0.1428	-0.174	1.2045	0.0014	-0.2278	0.3144	-0.0404	0.023	-0.0043	-0.2054	0.356	-0.0245	0.1627	-0.0896	-0.0861	0.1594	-0.0468	0.1727	15.696	10.836	183.664
2	0.7893	-0.1294	-0.4297	0.3249	-0.1712	1.3038	-0.1783	0.1525	0.0671	-0.033	0.0803	-0.0653	0.2163	-0.1059	0.098	0.1757	-0.0791	-0.0208	0.1186	0.0104	0.0303	0.443	-8.777	159.55
3	0.3348	-0.2366	-0.1744	0.3388	0.4415	1.2297	0.0726	-0.0612	-0.0127	0.0489	-0.0466	-0.016	0.4473	-0.2356	-0.0261	0.3304	-0.1403	-0.037	0.1498	0.0381	0.0178	37.738	-9.577	125.142
4	0.5577	0.0794	0.3578	0.5375	0.0464	0.9449	-0.0451	0.0087	0.0811	-0.001	0.0189	-0.089	-0.0562	0.1768	0.0262	0.1094	-0.0016	-0.0187	0.1532	-0.0114	0.0686	61.906	22.801	117.423
5	0.3462	-0.0448	0.29	0.509	0.3683	1.1975	0.0569	-0.1021	0.057	-0.1481	-0.146	0.0303	0.0273	-0.1812	0.089	0.157	0.0238	-0.0501	0.1365	-0.0326	0.041	31.554	12.756	99.901
6	0.1903	0.1613	0.4934	0.5231	0.4797	1.6378	0.0021	-0.2342	0.0875	-0.0694	-0.1835	0.0335	0.0736	-0.4629	0.1814	0.0652	-0.0094	-0.0042	0.3843	-0.1212	0.0501	36.366	22.402	140.954

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 316
2	X-RAY DIFFRACTION	1	A	401
3	X-RAY DIFFRACTION	2	B	3 - 318
4	X-RAY DIFFRACTION	2	B	401
5	X-RAY DIFFRACTION	3	C	3 - 317
6	X-RAY DIFFRACTION	3	C	401
7	X-RAY DIFFRACTION	4	D	4 - 317
8	X-RAY DIFFRACTION	4	D	401
9	X-RAY DIFFRACTION	5	E	4 - 317
10	X-RAY DIFFRACTION	5	E	401
11	X-RAY DIFFRACTION	6	F	3 - 318
12	X-RAY DIFFRACTION	6	F	401

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