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- PDB-4ln1: CRYSTAL STRUCTURE OF L-lactate dehydrogenase from Bacillus cereus... -

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Basic information

Entry
Database: PDB / ID: 4ln1
TitleCRYSTAL STRUCTURE OF L-lactate dehydrogenase from Bacillus cereus ATCC 14579 complexed with calcium, NYSGRC Target 029452
ComponentsL-lactate dehydrogenase 1
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / 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 / L-lactate dehydrogenase active site. / 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: 1.9 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 complexed with calcium, 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 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
C: L-lactate dehydrogenase 1
D: L-lactate dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,28310
Polymers151,0424
Non-polymers2406
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-144 kcal/mol
Surface area45120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.719, 75.453, 100.145
Angle α, β, γ (deg.)90.000, 89.990, 90.000
Int Tables number4
Space group name H-MP1211
Detailstetrameric

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Components

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


Mass: 37760.551 Da / Num. of mol.: 4
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ca-acetate, 0.1M sodium cacodylate:HCl, pH 6.5, 40% PEG300, 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: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.514
11h,-k,-l20.486
ReflectionResolution: 1.9→50 Å / Num. obs: 184605 / % possible obs: 95.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.064 / Χ2: 1.114 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9320.42691751.265195.4
1.93-1.9720.38991891.253195.8
1.97-2.0120.32392981.264195.7
2.01-2.0520.27993451.284195.9
2.05-2.0920.22393571.226196.2
2.09-2.1420.18892101.186196.3
2.14-2.1920.17292971.185196.3
2.19-2.2520.14793521.168196.2
2.25-2.3220.12592931.139196.1
2.32-2.3920.11293261.085196.5
2.39-2.4820.192871.069196.4
2.48-2.5820.08993051.056196.3
2.58-2.720.07793741.021196
2.7-2.841.90.07492431.015196.1
2.84-3.021.90.06392460.92195.3
3.02-3.251.90.05791301.014195
3.25-3.581.90.05491891.129194.6
3.58-4.091.90.04791090.994194.3
4.09-5.161.90.04391050.962194.1
5.16-501.90.04487750.986190.4

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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: PDB ENTRY 4LMR

4lmr


Resolution: 1.9→42.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2791 / WRfactor Rwork: 0.2455 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7409 / SU B: 6.399 / SU ML: 0.093 / SU R Cruickshank DPI: 0.0383 / SU Rfree: 0.0329 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4923 5 %RANDOM
Rwork0.2087 ---
obs0.2103 97912 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.48 Å2 / Biso mean: 41.8931 Å2 / Biso min: 19.63 Å2
Baniso -1Baniso -2Baniso -3
1--26.69 Å2-0 Å27.53 Å2
2--46.2 Å20 Å2
3----19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9936 0 6 351 10293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910179
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.97313811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85451276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28124.796465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.763151681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951551
X-RAY DIFFRACTIONr_chiral_restr0.0870.21574
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217663
X-RAY DIFFRACTIONr_mcbond_it1.1093.5465089
X-RAY DIFFRACTIONr_mcangle_it1.88747.7516355
X-RAY DIFFRACTIONr_scbond_it1.3713.8775090
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 367 -
Rwork0.266 6771 -
all-7138 -
obs--99.78 %
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)
11.02850.1886-0.30630.2688-0.14820.7125-0.0325-0.0309-0.2391-0.02050.0092-0.00780.2534-0.09580.02320.2793-0.04680.02180.02070.03170.24077.3365-4.175335.2457
21.167-0.0478-0.18960.22680.04111.1052-0.0570.0856-0.263-0.00030.01590.00910.27630.17980.04110.25960.05240.03530.0471-0.04660.224634.8819-4.06214.8341
31.2908-0.08750.1570.30720.07491.1549-0.1047-0.10530.3186-0.01430.00430.0068-0.32320.18140.10030.2645-0.0572-0.02360.0441-0.02560.223534.530525.679435.349
41.12280.09750.14410.27320.03791.0147-0.11090.14270.3380.00410.01010.03-0.3102-0.14280.10090.27630.0448-0.0320.0460.04760.25167.00425.24514.8671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 314
2X-RAY DIFFRACTION2B-6 - 314
3X-RAY DIFFRACTION3C-6 - 314
4X-RAY DIFFRACTION4D-6 - 314

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