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- PDB-4lmr: Crystal structure of L-lactate dehydrogenase from Bacillus cereus... -

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Basic information

Entry
Database: PDB / ID: 4lmr
TitleCrystal structure of L-lactate dehydrogenase from Bacillus cereus ATCC 14579, NYSGRC Target 029452
ComponentsL-lactate dehydrogenase 1Lactate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


lactate metabolic process / L-lactate dehydrogenase / L-lactate dehydrogenase activity / pyruvate metabolic process / 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
L-lactate dehydrogenase 1
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsMalashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. ...Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of L-lactate dehydrogenase from Bacillus cereus ATCC 14579, NYSGRC Target 029452
Authors: Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. ...Authors: Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Almo, S.C.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase 1
B: L-lactate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)75,5212
Polymers75,5212
Non-polymers00
Water2,396133
1
A: L-lactate dehydrogenase 1
B: L-lactate dehydrogenase 1

A: L-lactate dehydrogenase 1
B: L-lactate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)151,0424
Polymers151,0424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+3/2,-z+1/41
Buried area14970 Å2
ΔGint-84 kcal/mol
Surface area43260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.276, 177.276, 168.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21B-415-

HOH

Detailstetrameric

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Components

#1: Protein L-lactate dehydrogenase 1 / Lactate dehydrogenase / L-LDH 1


Mass: 37760.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_1924, ldh, ldh1 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q81EP4, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 4.39 Å3/Da / Density % sol: 72.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 3.5M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 94016 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.168 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.45-2.496.90.67446861.0381100
2.49-2.546.90.62246811.0511100
2.54-2.596.90.49947401.0681100
2.59-2.646.90.48847131.0641100
2.64-2.770.40646981.071100
2.7-2.767.10.3446701.0991100
2.76-2.837.10.28346831.1011100
2.83-2.97.20.23347531.1271100
2.9-2.997.30.19846601.1341100
2.99-3.097.40.1647051.1591100
3.09-3.27.50.12847011.1891100
3.2-3.327.50.10446831.2581100
3.32-3.487.60.08347251.1771100
3.48-3.667.60.07247071.2651100
3.66-3.897.60.06447161.2941100
3.89-4.197.60.06146851.4141100
4.19-4.617.60.0546821.3451100
4.61-5.287.50.04247061.2611100
5.28-6.657.50.03947101.1221100
6.65-507.80.03147121.06199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PQD

3pqd


Resolution: 2.45→46.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.1492 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8797 / SU B: 9.036 / SU ML: 0.098 / SU R Cruickshank DPI: 0.0377 / SU Rfree: 0.0312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 2470 5.1 %RANDOM
Rwork0.1631 ---
obs0.1639 48772 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.1 Å2 / Biso mean: 46.2424 Å2 / Biso min: 23.08 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å20 Å2
2--3.08 Å20 Å2
3----6.16 Å2
Refinement stepCycle: LAST / Resolution: 2.45→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 0 133 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194956
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.9746726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97524.865222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20915818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4291524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213726
X-RAY DIFFRACTIONr_mcbond_it2.2435.9152494
X-RAY DIFFRACTIONr_mcangle_it3.63879.673114
X-RAY DIFFRACTIONr_scbond_it3.7236.5362460
LS refinement shellResolution: 2.454→2.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 186 -
Rwork0.217 3268 -
all-3454 -
obs--96.86 %
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)
10.7179-0.13310.05620.4722-0.18380.62540.03980.0269-0.0343-0.0733-0.01080.00960.05140.0063-0.0290.0182-0.0048-0.01220.04130.04160.0491-11.807138.4513.6525
20.8559-0.0091-0.07761.0879-0.38660.57180.107-0.03530.07360.0079-0.1654-0.1723-0.07930.10.05840.0303-0.01710.00740.0760.07660.102117.0873151.020218.0178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 314
2X-RAY DIFFRACTION2B3 - 314

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