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- PDB-7xll: Alanine racemase from Lactobacillus sakei Uonuma-1. -

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Basic information

Entry
Database: PDB / ID: 7xll
TitleAlanine racemase from Lactobacillus sakei Uonuma-1.
ComponentsAlanine racemase
KeywordsISOMERASE / alanine racemase / PLP-dependent enzyme
Function / homologyACETATE ION / ALANINE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesLatilactobacillus sakei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsShimizu-Ibuka, A. / Kato, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: Regulation of alanine racemase activity by carboxylates and the d-type substrate d-alanine.
Authors: Shimizu-Ibuka, A. / Sato, A. / Ichimura, H. / Hiraga, H. / Nakayama, S. / Nishiwaki, T.
History
DepositionApr 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,45510
Polymers83,9052
Non-polymers5498
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-26 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.730, 125.040, 56.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Alanine racemase


Mass: 41952.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GB LC605911 / Source: (gene. exp.) Latilactobacillus sakei (bacteria) / Gene: C0213_08900 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: alanine racemase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 45.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 4000, Tris-HCl, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→62.52 Å / Num. obs: 76568 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.992 / Net I/σ(I): 9.8
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4267 / CC1/2: 0.794 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E5P

3e5p


Resolution: 1.76→62.52 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4236 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 3895 5.09 %random selection
Rwork0.1646 72580 --
obs0.1664 76475 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.39 Å2
Refinement stepCycle: LAST / Resolution: 1.76→62.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5864 0 37 862 6763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596135
X-RAY DIFFRACTIONf_angle_d0.82058356
X-RAY DIFFRACTIONf_chiral_restr0.0543924
X-RAY DIFFRACTIONf_plane_restr0.00511098
X-RAY DIFFRACTIONf_dihedral_angle_d5.84295591
LS refinement shellResolution: 1.76→1.78 Å
RfactorNum. reflection% reflection
Rfree0.2546 134 -
Rwork0.2325 2544 -
obs--98.82 %

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