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- PDB-8zph: SFX reaction state structure (40-60min) of alanine racemase -

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Basic information

Entry
Database: PDB / ID: 8zph
TitleSFX reaction state structure (40-60min) of alanine racemase
ComponentsAlanine racemase 2
KeywordsISOMERASE / Enzyme / substrate complex / peptidoglycan synthesis
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
ALANINE / PYRIDOXAL-5'-PHOSPHATE / Alanine racemase 2
Similarity search - Component
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)177,79814
Polymers176,4894
Non-polymers1,30910
Water1,42379
1
A: Alanine racemase 2
B: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8997
Polymers88,2452
Non-polymers6545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-46 kcal/mol
Surface area30920 Å2
MethodPISA
2
C: Alanine racemase 2
D: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8997
Polymers88,2452
Non-polymers6545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-45 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.200, 112.900, 91.800
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alanine racemase 2


Mass: 44122.312 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→67.32 Å / Num. obs: 146722 / % possible obs: 100 % / Redundancy: 463 % / CC1/2: 0.98 / CC star: 0.99 / R split: 0.21 / Net I/σ(I): 5.04
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 20700 / CC1/2: 0.26 / CC star: 0.43 / R split: 1.8
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→67.32 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 1028 0.7 %
Rwork0.201 --
obs0.2014 146722 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→67.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 76 79 12191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912322
X-RAY DIFFRACTIONf_angle_d1.04216640
X-RAY DIFFRACTIONf_dihedral_angle_d6.1161690
X-RAY DIFFRACTIONf_chiral_restr0.0581914
X-RAY DIFFRACTIONf_plane_restr0.0082086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.3911420.346520722X-RAY DIFFRACTION99
2.42-2.570.36711560.31820664X-RAY DIFFRACTION99
2.57-2.770.40451460.298520847X-RAY DIFFRACTION100
2.77-3.050.31331420.266120877X-RAY DIFFRACTION100
3.05-3.490.2981420.212920914X-RAY DIFFRACTION100
3.49-4.40.23461480.168320839X-RAY DIFFRACTION100
4.4-67.320.17771520.14820831X-RAY DIFFRACTION100

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