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- PDB-8zpe: SFX structure of the alanine racemase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 8zpe
TitleSFX structure of the alanine racemase from Bacillus subtilis
ComponentsAlanine racemase 2
KeywordsISOMERASE / apo enzyme / racemization
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / 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 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, J. / Nam, K.H. / Cho, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2024
Title: Exploring the reaction dynamics of alanine racemase using serial femtosecond crystallography.
Authors: Kim, J. / Park, J. / Lee, K. / Chung, W.K. / Nam, K.H. / Cho, Y.
History
DepositionMay 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine racemase 2
B: Alanine racemase 2
C: Alanine racemase 2
D: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,5448
Polymers177,4024
Non-polymers1424
Water3,927218
1
A: Alanine racemase 2
B: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7724
Polymers88,7012
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-49 kcal/mol
Surface area28020 Å2
MethodPISA
2
C: Alanine racemase 2
D: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7724
Polymers88,7012
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-49 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.600, 108.700, 89.100
Angle α, β, γ (deg.)90.00, 115.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alanine racemase 2


Mass: 44350.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: alr2, yncD, BSU17640 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P94494, alanine racemase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 100 mM Tris-Cl (pH 8.5), 0.25 M MgCl2, and 25% Peg 4K

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 0.979 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→79.39 Å / Num. obs: 132320 / % possible obs: 100 % / Redundancy: 335.85 % / CC1/2: 0.97 / CC star: 0.99 / R split: 0.19 / Net I/σ(I): 7.02
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 19407 / CC1/2: 0.47 / CC star: 0.63 / R split: 1.32
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MxDCdata collection
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q72

6q72


Resolution: 2.3→79.39 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2761 2.09 %
Rwork0.1782 --
obs0.1794 132320 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→79.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 64 218 12318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812312
X-RAY DIFFRACTIONf_angle_d0.93916628
X-RAY DIFFRACTIONf_dihedral_angle_d6.191688
X-RAY DIFFRACTIONf_chiral_restr0.0531912
X-RAY DIFFRACTIONf_plane_restr0.0082084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.37261330.3926443X-RAY DIFFRACTION100
2.34-2.380.39921350.35686462X-RAY DIFFRACTION100
2.38-2.430.34941550.29836502X-RAY DIFFRACTION100
2.43-2.480.2991250.27916478X-RAY DIFFRACTION100
2.48-2.530.29941470.25626501X-RAY DIFFRACTION100
2.53-2.590.29221370.24346408X-RAY DIFFRACTION100
2.59-2.660.32491290.25066553X-RAY DIFFRACTION100
2.66-2.730.28781310.23736441X-RAY DIFFRACTION100
2.73-2.810.31751470.23316479X-RAY DIFFRACTION100
2.81-2.90.271260.20286483X-RAY DIFFRACTION100
2.9-30.29921560.20466479X-RAY DIFFRACTION100
3-3.120.25791340.18386517X-RAY DIFFRACTION100
3.12-3.260.27341360.18646482X-RAY DIFFRACTION100
3.26-3.440.26411340.17676457X-RAY DIFFRACTION100
3.44-3.650.23941360.16996493X-RAY DIFFRACTION100
3.65-3.930.1951420.14166472X-RAY DIFFRACTION100
3.93-4.330.17551440.13426474X-RAY DIFFRACTION100
4.33-4.950.15091380.1246498X-RAY DIFFRACTION100
4.95-6.240.19071410.14996458X-RAY DIFFRACTION100
6.24-79.390.18791350.14346479X-RAY DIFFRACTION100

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