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- PDB-4prk: Crystal structure of D-lactate dehydrogenase (D-LDH) from Lactoba... -

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Basic information

Entry
Database: PDB / ID: 4prk
TitleCrystal structure of D-lactate dehydrogenase (D-LDH) 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 / :
Function and homology information
Biological speciesLactobacillus jensenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 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 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,2012
Polymers74,2012
Non-polymers00
Water1,76598
1
A: 4-phosphoerythronate dehydrogenase
B: 4-phosphoerythronate dehydrogenase

A: 4-phosphoerythronate dehydrogenase
B: 4-phosphoerythronate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)148,4024
Polymers148,4024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area13660 Å2
ΔGint-75 kcal/mol
Surface area52620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.532, 90.532, 157.780
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.52 Å3/Da / Density % sol: 51.1 % / Mosaicity: 0.68 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 400, Tris-HCl, MgSO4, pH 9.0, vapor diffusion, hanging drop, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)10.97985
SYNCHROTRONSPring-8 BL26B220.97919
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 270r1CCDNov 7, 2011Rh coated Torroidal Mirror
RAYONIX MX-2252CCDDec 13, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Fixed exit Si double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979851
20.979191
ReflectionRedundancy: 8.5 % / Number: 356502 / Rmerge(I) obs: 0.057 / Χ2: 1.15 / D res high: 2.13 Å / D res low: 50 Å / Num. obs: 41739 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.785099.110.0311.83811.7
4.595.7899.710.0371.50912.6
4.014.5999.510.0421.66512.6
3.644.0199.310.0521.69112.1
3.383.6499.410.061.47711.6
3.183.3899.410.0721.30810.8
3.023.1899.110.0851.1610.1
2.893.0299.110.1041.0119.3
2.782.8998.210.1190.9398.9
2.682.7898.710.1390.8658.4
2.62.6898.310.1550.8017.9
2.532.698.510.1770.7267.4
2.462.5398.410.1990.7237
2.42.4698.510.2240.6336.4
2.342.497.410.2390.66.1
2.292.3497.310.2420.5775.9
2.252.2997.710.2660.5585.5
2.212.2597.310.280.5355.3
2.172.2197.710.2790.4895.1
2.132.1783.510.2940.4474.2
ReflectionResolution: 2.13→50 Å / Num. obs: 41739 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 34.09 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.146 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1,2 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.13-2.174.20.29417580.44783.5
2.17-2.215.10.27920620.48997.7
2.21-2.255.30.2820440.53597.3
2.25-2.295.50.26620400.55897.7
2.29-2.345.90.24220360.57797.3
2.34-2.46.10.23920730.697.4
2.4-2.466.40.22420650.63398.5
2.46-2.5370.19920870.72398.4
2.53-2.67.40.17720610.72698.5
2.6-2.687.90.15520780.80198.3
2.68-2.788.40.13920820.86598.7
2.78-2.898.90.11920930.93998.2
2.89-3.029.30.10421211.01199.1
3.02-3.1810.10.08520871.1699.1
3.18-3.3810.80.07221291.30899.4
3.38-3.6411.60.0621371.47799.4
3.64-4.0112.10.05221231.69199.3
4.01-4.5912.60.04221601.66599.5
4.59-5.7812.60.03721891.50999.7
5.78-5011.70.03123141.83899.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
RESOLVEphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.13→38.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.314 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 2110 5.1 %RANDOM
Rwork0.215 ---
all0.25 41723 --
obs0.2306 39613 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.65 Å2 / Biso mean: 45.104 Å2 / Biso min: 18.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å2-0 Å2
2---0.15 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.13→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 0 98 5168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195154
X-RAY DIFFRACTIONr_bond_other_d0.0010.025060
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9746978
X-RAY DIFFRACTIONr_angle_other_deg0.829311678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43825.472212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12515926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3351516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021062
X-RAY DIFFRACTIONr_mcbond_it3.1554.292630
X-RAY DIFFRACTIONr_mcbond_other3.154.2892629
X-RAY DIFFRACTIONr_mcangle_it4.476.423284
LS refinement shellResolution: 2.133→2.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 148 -
Rwork0.307 2765 -
all-2913 -
obs--94.61 %

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