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

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Basic information

Entry
Database: PDB / ID: 6j9t
TitleComplex structure of Lactobacillus casei lactate dehydrogenase with fructose-1,6-bisphosphate
ComponentsL-lactate dehydrogenaseLactate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase active site. / L-lactate dehydrogenase / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / L-lactate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus casei subsp. casei ATCC 393 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsArai, K. / Miyanaga, A. / Uchikoba, H. / Fushinobu, S. / Taguchi, H.
CitationJournal: 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
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 6, 2019ID: 3VKV
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: 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 1.2Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)215,01915
Polymers213,4236
Non-polymers1,5979
Water1,982110
1
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,34610
Polymers142,2824
Non-polymers1,0646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area18000 Å2
ΔGint-175 kcal/mol
Surface area42740 Å2
MethodPISA
2
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
E: L-lactate dehydrogenase
F: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,34610
Polymers142,2824
Non-polymers1,0646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17820 Å2
ΔGint-165 kcal/mol
Surface area42480 Å2
MethodPISA
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 number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAAA3 - 3163 - 316
21SERSERALAALABB3 - 3163 - 316
12SERSERASPASPAA3 - 3153 - 315
22SERSERASPASPCC3 - 3153 - 315
13ILEILEALAALAAA4 - 3164 - 316
23ILEILEALAALADD4 - 3164 - 316
14ILEILEALAALAAA4 - 3164 - 316
24ILEILEALAALAEE4 - 3164 - 316
15SERSERALAALAAA3 - 3163 - 316
25SERSERALAALAFF3 - 3163 - 316
16SERSERPHEPHEBB3 - 3173 - 317
26SERSERPHEPHECC3 - 3173 - 317
17ILEILEALAALABB4 - 3164 - 316
27ILEILEALAALADD4 - 3164 - 316
18ILEILEPHEPHEBB4 - 3174 - 317
28ILEILEPHEPHEEE4 - 3174 - 317
19SERSERALAALABB3 - 3183 - 318
29SERSERALAALAFF3 - 3183 - 318
110ILEILEPHEPHECC4 - 3174 - 317
210ILEILEPHEPHEDD4 - 3174 - 317
111ILEILEPHEPHECC4 - 3174 - 317
211ILEILEPHEPHEEE4 - 3174 - 317
112SERSERPHEPHECC3 - 3173 - 317
212SERSERPHEPHEFF3 - 3173 - 317
113ILEILEPHEPHEDD4 - 3174 - 317
213ILEILEPHEPHEEE4 - 3174 - 317
114ILEILEALAALADD4 - 3164 - 316
214ILEILEALAALAFF4 - 3164 - 316
115ILEILEPHEPHEEE4 - 3174 - 317
215ILEILEPHEPHEFF4 - 3174 - 317

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

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Components

#1: Protein
L-lactate dehydrogenase / 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 / Sulfate


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 / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 67283 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2 / Num. unique obs: 9734 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZQZ

2zqz


Resolution: 2.7→41.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 3405 5.1 %RANDOM
Rwork0.19556 ---
obs0.19712 63871 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20.15 Å2
2--0.15 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.7→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14375 0 90 110 14575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01914715
X-RAY DIFFRACTIONr_bond_other_d0.0080.0214288
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9719981
X-RAY DIFFRACTIONr_angle_other_deg1.28332938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7751866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12525.486607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.728152538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2791548
X-RAY DIFFRACTIONr_chiral_restr0.0810.22332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216518
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023072
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194720.06
12B194720.06
21A193120.07
22C193120.07
31A192560.08
32D192560.08
41A189610.07
42E189610.07
51A195010.06
52F195010.06
61B194570.07
62C194570.07
71B192540.08
72D192540.08
81B191370.07
82E191370.07
91B197630.07
92F197630.07
101C192970.08
102D192970.08
111C189830.07
112E189830.07
121C194480.07
122F194480.07
131D191700.08
132E191700.08
141D193710.08
142F193710.08
151E192560.06
152F192560.06
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 262 -
Rwork0.279 4664 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.89090.0471-0.48720.1428-0.1741.20450.0014-0.22780.3144-0.04040.023-0.0043-0.20540.356-0.02450.1627-0.0896-0.08610.1594-0.04680.172715.69610.836183.664
20.7893-0.1294-0.42970.3249-0.17121.3038-0.17830.15250.0671-0.0330.0803-0.06530.2163-0.10590.0980.1757-0.0791-0.02080.11860.01040.03030.443-8.777159.55
30.3348-0.2366-0.17440.33880.44151.22970.0726-0.0612-0.01270.0489-0.0466-0.0160.4473-0.2356-0.02610.3304-0.1403-0.0370.14980.03810.017837.738-9.577125.142
40.55770.07940.35780.53750.04640.9449-0.04510.00870.0811-0.0010.0189-0.089-0.05620.17680.02620.1094-0.0016-0.01870.1532-0.01140.068661.90622.801117.423
50.3462-0.04480.290.5090.36831.19750.0569-0.10210.057-0.1481-0.1460.03030.0273-0.18120.0890.1570.0238-0.05010.1365-0.03260.04131.55412.75699.901
60.19030.16130.49340.52310.47971.63780.0021-0.23420.0875-0.0694-0.18350.03350.0736-0.46290.18140.0652-0.0094-0.00420.3843-0.12120.050136.36622.402140.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 316
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B3 - 318
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C3 - 317
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D4 - 317
8X-RAY DIFFRACTION4D401
9X-RAY DIFFRACTION5E4 - 317
10X-RAY DIFFRACTION5E401
11X-RAY DIFFRACTION6F3 - 318
12X-RAY DIFFRACTION6F401

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