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

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Basic information

Entry
Database: PDB / ID: 9eia
TitleA broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with copurified D-lactate
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 / LACTIC ACID / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesIsosphaera pallida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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

Downloads & links

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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)93,39214
Polymers91,7982
Non-polymers1,59512
Water9,296516
1
A: A broad-substrate spectrum lactate racemase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6747
Polymers45,8991
Non-polymers7756
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)46,7187
Polymers45,8991
Non-polymers8196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.420, 45.514, 119.140
Angle α, β, γ (deg.)90.00, 91.20, 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, 528 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 2 / Source method: obtained synthetically / Formula: C12H15NO8PS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / 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.: 516 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
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 ethylene glycols (diethylene glycol, triethylene glycol, tetraethylene glycol and pentaethylene glycol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127231 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127231 Å / Relative weight: 1
ReflectionResolution: 1.74→33.07 Å / Num. obs: 84457 / % possible obs: 96.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.083 / Net I/σ(I): 10.3
Reflection shellResolution: 1.74→1.8 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 8214 / CC1/2: 0.61 / Rpim(I) all: 0.469

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→33.07 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 4103 4.86 %
Rwork0.1738 --
obs0.1757 84408 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 95 516 6899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076585
X-RAY DIFFRACTIONf_angle_d0.9829025
X-RAY DIFFRACTIONf_dihedral_angle_d13.704940
X-RAY DIFFRACTIONf_chiral_restr0.0641084
X-RAY DIFFRACTIONf_plane_restr0.0071163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.3471120.31132485X-RAY DIFFRACTION84
1.76-1.780.3231490.27152581X-RAY DIFFRACTION94
1.78-1.80.28871620.25792764X-RAY DIFFRACTION95
1.8-1.830.25451600.232749X-RAY DIFFRACTION97
1.83-1.850.25391640.21282791X-RAY DIFFRACTION98
1.85-1.880.2871570.21012744X-RAY DIFFRACTION97
1.88-1.910.24421310.19732872X-RAY DIFFRACTION98
1.91-1.940.24611400.18742779X-RAY DIFFRACTION98
1.94-1.970.20011570.18222845X-RAY DIFFRACTION98
1.97-20.22361460.17522766X-RAY DIFFRACTION98
2-2.040.24531600.18032818X-RAY DIFFRACTION97
2.04-2.080.23091470.18282813X-RAY DIFFRACTION97
2.08-2.120.20631370.18472767X-RAY DIFFRACTION98
2.12-2.170.24031320.17892792X-RAY DIFFRACTION95
2.17-2.220.23741470.17752636X-RAY DIFFRACTION94
2.22-2.270.22491250.18112489X-RAY DIFFRACTION85
2.27-2.330.21021410.17352670X-RAY DIFFRACTION93
2.33-2.40.21991320.16672907X-RAY DIFFRACTION99
2.4-2.480.211530.16742818X-RAY DIFFRACTION99
2.48-2.570.19371620.16652831X-RAY DIFFRACTION99
2.57-2.670.22281320.16512869X-RAY DIFFRACTION98
2.67-2.790.22561430.17112858X-RAY DIFFRACTION99
2.79-2.940.21531310.17382853X-RAY DIFFRACTION97
2.94-3.120.22351370.17882807X-RAY DIFFRACTION97
3.13-3.370.21331220.16662862X-RAY DIFFRACTION97
3.37-3.70.16411240.15882759X-RAY DIFFRACTION95
3.7-4.240.16841250.14242545X-RAY DIFFRACTION86
4.24-5.340.17241480.14132838X-RAY DIFFRACTION96
5.34-33.070.17711270.16952997X-RAY DIFFRACTION97

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