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

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Basic information

Entry
Database: PDB / ID: 9eid
TitleA broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxybutyrate
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, N-terminal / LarA-like, C-terminal domain / : / Lactate racemase N-terminal domain
Similarity search - Domain/homology
Chem-4EY / NICKEL (II) ION / PHOSPHATE ION / (2R)-2-oxidanylbutanoic acid / Uncharacterized protein
Similarity search - Component
Biological speciesIsosphaera pallida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6066
Polymers45,8571
Non-polymers7495
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.725, 79.613, 104.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 45856.727 Da / Num. of mol.: 1
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 , 5 types, 533 molecules

#2: Chemical ChemComp-UCU / (2R)-2-oxidanylbutanoic acid / (R)-2-Hydroxybutanoic acid


Mass: 104.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 1 / Source method: obtained synthetically / Formula: C12H15NO8PS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris buffer pH 6.0, 25% PEG 5000, and 2.8 mM Sodium D/L-2-hydroxybutyrate

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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: Mar 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.38→29.11 Å / Num. obs: 80218 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.099 / Net I/σ(I): 18.6
Reflection shellResolution: 1.38→1.41 Å / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3732 / CC1/2: 0.805 / Rpim(I) all: 0.288 / Rrim(I) all: 0.818

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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: 1.38→29.11 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1662 3987 4.98 %
Rwork0.1513 --
obs0.1521 80127 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 42 528 3769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063410
X-RAY DIFFRACTIONf_angle_d0.994691
X-RAY DIFFRACTIONf_dihedral_angle_d19.343491
X-RAY DIFFRACTIONf_chiral_restr0.088557
X-RAY DIFFRACTIONf_plane_restr0.006609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.23751350.21722550X-RAY DIFFRACTION94
1.4-1.420.22861480.2022638X-RAY DIFFRACTION98
1.42-1.440.18211300.1912646X-RAY DIFFRACTION100
1.44-1.460.22341550.17792707X-RAY DIFFRACTION100
1.46-1.480.18321670.16922673X-RAY DIFFRACTION100
1.48-1.50.15561270.16262698X-RAY DIFFRACTION100
1.5-1.520.17061570.15772662X-RAY DIFFRACTION100
1.52-1.550.22871310.15232735X-RAY DIFFRACTION100
1.55-1.580.18631310.152690X-RAY DIFFRACTION100
1.58-1.60.17311520.14832678X-RAY DIFFRACTION100
1.6-1.630.17541230.14532711X-RAY DIFFRACTION100
1.63-1.670.16571370.14592748X-RAY DIFFRACTION100
1.67-1.70.1571430.14012678X-RAY DIFFRACTION100
1.7-1.740.16961290.14412737X-RAY DIFFRACTION100
1.74-1.790.16491310.1452716X-RAY DIFFRACTION100
1.79-1.840.16221290.14832720X-RAY DIFFRACTION100
1.84-1.890.16341410.15372716X-RAY DIFFRACTION100
1.89-1.950.18661360.15182744X-RAY DIFFRACTION100
1.95-2.020.18611440.15012722X-RAY DIFFRACTION100
2.02-2.10.15941700.14932698X-RAY DIFFRACTION100
2.1-2.20.16071500.14542706X-RAY DIFFRACTION100
2.2-2.310.17451570.1532735X-RAY DIFFRACTION100
2.31-2.460.17171520.15472737X-RAY DIFFRACTION100
2.46-2.650.17021410.15662763X-RAY DIFFRACTION100
2.65-2.910.1631510.16012759X-RAY DIFFRACTION100
2.91-3.330.19071380.15662790X-RAY DIFFRACTION100
3.33-4.20.12931190.13542846X-RAY DIFFRACTION100
4.2-29.110.12781630.13612937X-RAY DIFFRACTION100

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