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- PDB-5zl6: Histidine Racemase from Leuconostoc mesenteroides subsp. sake NBR... -

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Basic information

Entry
Database: PDB / ID: 5zl6
TitleHistidine Racemase from Leuconostoc mesenteroides subsp. sake NBRC 102480
ComponentsHistidine racemase
KeywordsISOMERASE / Histidine / Racemase / Dimer / PLP
Function / homology
Function and homology information


alanine metabolic process / alanine racemase / alanine racemase activity
Similarity search - Function
Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel ...Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Alanine racemase
Similarity search - Component
Biological speciesLeuconostoc mesenteroides subsp. sake (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAdachi, M. / Shimizu, R. / Oikawa, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16KT0063 Japan
CitationJournal: Amino Acids / Year: 2019
Title: The first identification and characterization of a histidine-specific amino acid racemase, histidine racemase from a lactic acid bacterium, Leuconostoc mesenteroides subsp. sake NBRC 102480.
Authors: Adachi, M. / Shimizu, R. / Kato, S. / Oikawa, T.
History
DepositionMar 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine racemase
B: Histidine racemase
C: Histidine racemase
D: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,42010
Polymers165,9374
Non-polymers1,4836
Water39,4712191
1
A: Histidine racemase
B: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7105
Polymers82,9692
Non-polymers7413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-20 kcal/mol
Surface area26380 Å2
MethodPISA
2
C: Histidine racemase
D: Histidine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7105
Polymers82,9692
Non-polymers7413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-13 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.048, 142.468, 78.701
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Histidine racemase


Mass: 41484.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc mesenteroides subsp. sake (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03Z32*PLUS
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) polyethylene glycol 4000, 5% (w/v) glycerol, 200 mM magnesium chloride and a 100 mM Tris-HCl buffer (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→33.6 Å / Num. obs: 84173 / % possible obs: 98.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 8174 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CO8

3co8


Resolution: 2.1→33.6 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 23.73
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4207 5 %Random selecttion
Rwork0.174 ---
obs0.177 84128 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11324 0 90 2192 13606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511652
X-RAY DIFFRACTIONf_angle_d1.03315860
X-RAY DIFFRACTIONf_dihedral_angle_d15.8064220
X-RAY DIFFRACTIONf_chiral_restr0.041840
X-RAY DIFFRACTIONf_plane_restr0.0052044
LS refinement shellResolution: 2.1008→2.1246 Å
RfactorNum. reflection% reflection
Rfree0.3409 122 5 %
Rwork0.2444 --
obs-2320 84 %

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