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- PDB-6q72: Crystal structure of the alanine racemase from Bacillus subtilis ... -

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Basic information

Entry
Database: PDB / ID: 6q72
TitleCrystal structure of the alanine racemase from Bacillus subtilis in the presence of only PEG 4000 and Magnesium chloride in the crystallization condition
ComponentsAlanine racemase 2
KeywordsISOMERASE / racemase / alanine racemase
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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 ...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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / : / Alanine racemase 2
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBernardo-Garcia, N. / Gago, F. / Hermoso, J.A.
CitationJournal: Org.Biomol.Chem. / Year: 2019
Title: Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.
Authors: Bernardo-Garcia, N. / Sanchez-Murcia, P.A. / Espaillat, A. / Martinez-Caballero, S. / Cava, F. / Hermoso, J.A. / Gago, F.
History
DepositionDec 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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: Alanine racemase 2
B: Alanine racemase 2
D: Alanine racemase 2
E: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,96612
Polymers174,8354
Non-polymers1,1308
Water1267
1
A: Alanine racemase 2
B: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9836
Polymers87,4182
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-55 kcal/mol
Surface area28780 Å2
MethodPISA
2
D: Alanine racemase 2
E: Alanine racemase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9836
Polymers87,4182
Non-polymers5654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-51 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.431, 110.526, 88.507
Angle α, β, γ (deg.)90.00, 116.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alanine racemase 2


Mass: 43708.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: D3Z87_09640 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A386RMP5, UniProt: P94494*PLUS
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 35.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 290 K / Method: microbatch / Details: 15% PEG 4000, 0.2 MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.85→46.61 Å / Num. obs: 35532 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 5.7
Reflection shellResolution: 2.85→2.99 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
APEX 2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5RIP

5rip
PDB Unreleased entry


Resolution: 3→45.32 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.59
RfactorNum. reflection% reflection
Rfree0.2851 1522 5.01 %
Rwork0.2275 --
obs0.2303 30360 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12100 0 4 7 12111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01512326
X-RAY DIFFRACTIONf_angle_d1.55316654
X-RAY DIFFRACTIONf_dihedral_angle_d15.957446
X-RAY DIFFRACTIONf_chiral_restr0.0931912
X-RAY DIFFRACTIONf_plane_restr0.0072088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09680.34751240.33982627X-RAY DIFFRACTION100
3.0968-3.20750.39191490.31422629X-RAY DIFFRACTION100
3.2075-3.33590.34451550.28552593X-RAY DIFFRACTION100
3.3359-3.48760.33881510.28032617X-RAY DIFFRACTION100
3.4876-3.67140.41321600.31992572X-RAY DIFFRACTION98
3.6714-3.90130.31011690.25952501X-RAY DIFFRACTION97
3.9013-4.20240.27851480.22742639X-RAY DIFFRACTION100
4.2024-4.62490.24041410.1832638X-RAY DIFFRACTION99
4.6249-5.29320.20081130.17572635X-RAY DIFFRACTION99
5.2932-6.66550.26041070.20392685X-RAY DIFFRACTION99
6.6655-45.32510.20371050.17682702X-RAY DIFFRACTION98

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