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- PDB-4prl: Crystal structure of D-lactate dehydrogenase with NAD+ from Lacto... -

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Basic information

Entry
Database: PDB / ID: 4prl
TitleCrystal structure of D-lactate dehydrogenase with NAD+ from Lactobacillus jensenii
Components4-phosphoerythronate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesLactobacillus jensenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKim, S. / Kim, K.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2014
Title: Crystal structure and thermodynamic properties of d-lactate dehydrogenase from Lactobacillus jensenii.
Authors: Kim, S. / Gu, S.A. / Kim, Y.H. / Kim, K.J.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-phosphoerythronate dehydrogenase
B: 4-phosphoerythronate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5284
Polymers74,2012
Non-polymers1,3272
Water52229
1
A: 4-phosphoerythronate dehydrogenase
B: 4-phosphoerythronate dehydrogenase
hetero molecules

A: 4-phosphoerythronate dehydrogenase
B: 4-phosphoerythronate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,0568
Polymers148,4024
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area18290 Å2
ΔGint-98 kcal/mol
Surface area52490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.714, 90.714, 158.183
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 4-phosphoerythronate dehydrogenase


Mass: 37100.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus jensenii (bacteria) / Gene: pdxB, LBJG_01197 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: C5G4U0, 4-phosphoerythronate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.53 Å3/Da / Density % sol: 51.42 % / Mosaicity: 0.72 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 400, Tris-HCl, MgSO4, NADH, pH 9.0, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97985 Å
DetectorType: ADSC QUANTUM 270r / Detector: CCD / Date: Nov 8, 2011 / Details: Rh coated Torroidal Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Rmerge(I) obs: 0.078 / Χ2: 1.18 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 23041 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.055098.310.0382.2725.5
5.67.0598.310.0491.2655.5
4.895.698.510.0541.4775.7
4.454.8998.810.0561.6035.7
4.134.4598.710.061.5745.6
3.884.139910.0731.4925.3
3.693.8897.810.081.3425.2
3.533.6998.110.0941.1654.9
3.393.5397.510.1151.0594.7
3.283.3997.810.130.9344.5
3.173.2897.210.1510.9164.3
3.083.1796.710.170.8364
33.0895.410.2030.7573.8
2.9339410.2170.6593.5
2.862.9396.110.2360.6723.6
2.82.8694.610.2440.6053.3
2.742.894.310.2710.5953.2
2.692.7493.810.2940.63.1
2.642.6992.810.2940.553
2.62.6490.910.3090.5442.9
ReflectionResolution: 2.6→50 Å / Num. obs: 23041 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 40.22 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.185 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.642.90.30910560.54490.9
2.64-2.6930.29410920.5592.8
2.69-2.743.10.29410980.693.8
2.74-2.83.20.27111050.59594.3
2.8-2.863.30.24411310.60594.6
2.86-2.933.60.23611240.67296.1
2.93-33.50.21710890.65994
3-3.083.80.20311280.75795.4
3.08-3.1740.1711270.83696.7
3.17-3.284.30.15111640.91697.2
3.28-3.394.50.1311540.93497.8
3.39-3.534.70.11511531.05997.5
3.53-3.694.90.09411661.16598.1
3.69-3.885.20.0811681.34297.8
3.88-4.135.30.07312001.49299
4.13-4.455.60.0611821.57498.7
4.45-4.895.70.05611851.60398.8
4.89-5.65.70.05412001.47798.5
5.6-7.055.50.04912211.26598.3
7.05-505.50.03812982.27298.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRK

4prk


Resolution: 2.6→30.12 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.863 / SU B: 14.649 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.304 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1178 5.1 %RANDOM
Rwork0.2106 ---
all0.264 22940 --
obs0.2279 21762 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.07 Å2 / Biso mean: 51.361 Å2 / Biso min: 21.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 88 29 5209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195274
X-RAY DIFFRACTIONr_bond_other_d0.0010.025130
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9967156
X-RAY DIFFRACTIONr_angle_other_deg0.811311838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92825.327214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86715932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0021518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021100
X-RAY DIFFRACTIONr_mcbond_it2.714.9292638
X-RAY DIFFRACTIONr_mcbond_other2.7054.9262637
X-RAY DIFFRACTIONr_mcangle_it4.3367.3793294
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 87 -
Rwork0.311 1496 -
all-1583 -
obs--91.45 %

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