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- PDB-8ezf: A tethered niacin-derived pincer complex with a nickel-carbon or ... -

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Basic information

Entry
Database: PDB / ID: 8ezf
TitleA tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase R98A/R100A variant
ComponentsLactate racemase
KeywordsISOMERASE / Catalytic activity / isomerase activity / racemase and epimerase activity racemase acting on hydroxy acids and derivatives / metal ion binding
Function / homology
Function and homology information


lactate racemase / lactate racemase activity / metal ion binding
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-ENJ / NICKEL (II) ION / Lactate racemase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGatreddi, S. / Hausinger, R.P. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1807073 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128959 United States
CitationJournal: Acs Catalysis / Year: 2023
Title: Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor.
Authors: Gatreddi, S. / Sui, D. / Hausinger, R.P. / Hu, J.
History
DepositionOct 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lactate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,59820
Polymers47,1531
Non-polymers1,44519
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.840, 79.913, 121.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Lactate racemase / Lar / Lactate racemization operon protein LarA


Mass: 47153.289 Da / Num. of mol.: 1 / Mutation: R98A, R100A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larA, lp_0104 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: F9USS9, lactate racemase

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Non-polymers , 7 types, 194 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ENJ / (4S)-5-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-4-sulfo-1,4-dihydropyridine-3-carbothioic S-acid


Mass: 477.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16NO11PS3 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Sodium HEPES/MOPS (pH 7.5), 60 mM Magnesium chloride hexahydrate, 60 mM Calcium chloride dihydrate, 20% Ethylene glycol and 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→37.97 Å / Num. obs: 23345 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1921 / Rpim(I) all: 0.45 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUQ

5huq


Resolution: 2.15→37.97 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 1152 4.94 %
Rwork0.1864 22180 -
obs0.1892 23332 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.43 Å2 / Biso mean: 27.6493 Å2 / Biso min: 9.49 Å2
Refinement stepCycle: final / Resolution: 2.15→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 86 175 3392
Biso mean--27.18 33.92 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.250.3141420.23432657279998
2.25-2.370.30331230.214727552878100
2.37-2.520.24221460.19127372883100
2.52-2.710.24981320.186827532885100
2.71-2.980.23661480.18327442892100
2.98-3.420.26041560.172627672923100
3.42-4.30.21111460.162428342980100
4.3-37.970.23191590.197629333092100

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