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- PDB-8ezi: A tethered niacin-derived pincer complex with a nickel-carbon bon... -

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Basic information

Entry
Database: PDB / ID: 8ezi
TitleA tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase R98A/R100A variant modeled with separated sulfite and NPN
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-4EY / NICKEL (II) ION / SULFITE ION / Lactate racemase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 2.0May 1, 2024Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Lactate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23416
Polymers47,1531
Non-polymers1,08115
Water3,765209
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)43.011, 79.092, 121.171
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 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 , 8 types, 224 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Sodium HEPES/MOPS (pH 7.5), 60 mM Magnesium chloride hexahydrate, 60 mM Calcium chloride dihydrate, 27% Ethylene glycol and 14% 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: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.99→37.79 Å / Num. obs: 29029 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.74 / Rpim(I) all: 0.24 / Net I/σ(I): 9.1
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 9.1 % / Rmerge(I) obs: 4.7 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2074 / Rpim(I) all: 1.62 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EZF

8ezf


Resolution: 1.99→37.79 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1418 4.89 %
Rwork0.1825 --
obs0.1845 29024 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 56 209 3378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083280
X-RAY DIFFRACTIONf_angle_d1.014457
X-RAY DIFFRACTIONf_dihedral_angle_d16.093460
X-RAY DIFFRACTIONf_chiral_restr0.062516
X-RAY DIFFRACTIONf_plane_restr0.006581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.060.24841330.22322669X-RAY DIFFRACTION98
2.06-2.150.30731260.22592751X-RAY DIFFRACTION100
2.15-2.240.28361370.20922705X-RAY DIFFRACTION100
2.24-2.360.24141520.20512712X-RAY DIFFRACTION100
2.36-2.510.24991220.19482751X-RAY DIFFRACTION100
2.51-2.70.2361420.18632747X-RAY DIFFRACTION100
2.7-2.970.24831230.19232770X-RAY DIFFRACTION100
2.98-3.40.23641540.1842772X-RAY DIFFRACTION100
3.41-4.290.17361580.15162802X-RAY DIFFRACTION100
4.29-37.790.19181710.1642927X-RAY DIFFRACTION100

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