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- PDB-9eif: A broad-substrate spectrum lactate racemase A from Isosphaera pal... -

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Basic information

Entry
Database: PDB / ID: 9eif
TitleA broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxyisovalerate
ComponentsA broad-substrate spectrum lactate racemase A
KeywordsISOMERASE / Catalytic activity / isomerase activity / racemase and epimerase activity racemase acting on hydroxy acids and derivatives
Function / homology
Function and homology information


lactate racemase activity
Similarity search - Function
: / : / Lactate racemase C-terminal domain / LarA-like, C-terminal domain / LarA-like, N-terminal / : / Lactate racemase N-terminal domain
Similarity search - Domain/homology
Chem-4EY / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DEAMINOHYDROXYVALINE / Uncharacterized protein
Similarity search - Component
Biological speciesIsosphaera pallida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGatreddi, S. / Hausinger, R.P. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140931 United States
CitationJournal: Biorxiv / Year: 2024
Title: Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum.
Authors: Gatreddi, S. / Urdiain-Arraiza, J. / Desguin, B. / Hausinger, R.P. / Hu, J.
History
DepositionNov 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A broad-substrate spectrum lactate racemase A
B: A broad-substrate spectrum lactate racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,30611
Polymers91,7982
Non-polymers1,5099
Water11,440635
1
A: A broad-substrate spectrum lactate racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8347
Polymers45,8991
Non-polymers9366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A broad-substrate spectrum lactate racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4724
Polymers45,8991
Non-polymers5733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.024, 45.246, 118.218
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein A broad-substrate spectrum lactate racemase A


Mass: 45898.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Isosphaera pallida (bacteria) / Gene: Isop_3476 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ3900 / References: UniProt: E8QWZ4

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Non-polymers , 6 types, 644 molecules

#2: Chemical ChemComp-4EY / 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium / Dithiodinicotinic acid mononucleotide


Mass: 396.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO8PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-VAD / DEAMINOHYDROXYVALINE


Type: L-peptide linking / Mass: 118.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Imidazole/MES monohydrate, pH 6.5, 20 % PEG 500 MME, 20% PEG 20,000, and 120 mM each of monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D- ...Details: 0.1 M Imidazole/MES monohydrate, pH 6.5, 20 % PEG 500 MME, 20% PEG 20,000, and 120 mM each of monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D-Glucosamine), and 3 mM D-2-hydroxyisovaleric acid (pH adjusted with 95 mM NaOH, pH ~7-8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→29.71 Å / Num. obs: 100330 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Net I/σ(I): 10.9
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4682 / CC1/2: 0.762 / Rpim(I) all: 0.291 / Rrim(I) all: 0.774 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.71 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 10039 5.15 %
Rwork0.166 --
obs0.1673 100303 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6342 0 90 635 7067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076694
X-RAY DIFFRACTIONf_angle_d1.0159187
X-RAY DIFFRACTIONf_dihedral_angle_d14.891957
X-RAY DIFFRACTIONf_chiral_restr0.0671096
X-RAY DIFFRACTIONf_plane_restr0.0071189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.29283300.25895721X-RAY DIFFRACTION92
1.67-1.690.27653320.2556241X-RAY DIFFRACTION99
1.69-1.710.29843060.24716105X-RAY DIFFRACTION99
1.71-1.730.24692790.24316177X-RAY DIFFRACTION98
1.73-1.750.23813550.22836072X-RAY DIFFRACTION98
1.75-1.780.2433100.22146143X-RAY DIFFRACTION100
1.78-1.80.27423340.2136189X-RAY DIFFRACTION98
1.8-1.830.22773330.20346160X-RAY DIFFRACTION99
1.83-1.860.21333130.19796204X-RAY DIFFRACTION100
1.86-1.890.22083080.18966143X-RAY DIFFRACTION97
1.89-1.920.20493930.18936105X-RAY DIFFRACTION100
1.92-1.960.21443390.186210X-RAY DIFFRACTION99
1.96-1.990.20043560.17026068X-RAY DIFFRACTION99
1.99-2.030.21983000.1656328X-RAY DIFFRACTION100
2.03-2.080.20013210.16676146X-RAY DIFFRACTION98
2.08-2.130.19583320.166196X-RAY DIFFRACTION100
2.13-2.180.20313600.15686127X-RAY DIFFRACTION99
2.18-2.240.19152940.15976248X-RAY DIFFRACTION100
2.24-2.30.1863240.15916145X-RAY DIFFRACTION99
2.3-2.380.19513480.15726283X-RAY DIFFRACTION100
2.38-2.460.20613790.15586150X-RAY DIFFRACTION100
2.46-2.560.18863290.15346180X-RAY DIFFRACTION99
2.56-2.680.17863590.15466228X-RAY DIFFRACTION100
2.68-2.820.18193300.15556226X-RAY DIFFRACTION100
2.82-30.17483970.16196167X-RAY DIFFRACTION100
3-3.230.1933760.16286152X-RAY DIFFRACTION100
3.23-3.550.16183400.15386212X-RAY DIFFRACTION100
3.55-4.070.15412620.13916316X-RAY DIFFRACTION100
4.07-5.120.14243040.13196264X-RAY DIFFRACTION100
5.12-29.710.16763960.16036136X-RAY DIFFRACTION100

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