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- PDB-4luy: Crystal structure of CdALR mutant K 271 T -

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Basic information

Entry
Database: PDB / ID: 4luy
TitleCrystal structure of CdALR mutant K 271 T
ComponentsAlanine racemase
KeywordsISOMERASE / 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 / 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, 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 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / 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
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAsojo, O.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630.
Authors: Asojo, O.A. / Nelson, S.K. / Mootien, S. / Lee, Y. / Rezende, W.C. / Hyman, D.A. / Matsumoto, M.M. / Reiling, S. / Kelleher, A. / Ledizet, M. / Koski, R.A. / Anthony, K.G.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alanine racemase
B: Alanine racemase


Theoretical massNumber of molelcules
Total (without water)87,2162
Polymers87,2162
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-29 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.970, 154.330, 55.770
Angle α, β, γ (deg.)90.00, 113.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alanine racemase


Mass: 43607.988 Da / Num. of mol.: 2 / Mutation: K271T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: alr2, CD630_34630 / Production host: Escherichia coli (E. coli) / References: UniProt: Q180W0, alanine racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17M LiSO4, 0.085M Tris-HCL pH 8.5, 25.5% PEG4000, 15.5% Glycerol, 0.02% betamercaptoethanol, 10 mM PLP , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→45.59 Å / Num. all: 22586 / Num. obs: 21924 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 4.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 1.9 / % possible all: 55.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LUS

4lus


Resolution: 2.6→28.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.13 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25199 1182 5.1 %RANDOM
Rwork0.18133 ---
obs0.18498 21910 97.13 %-
all-22586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.878 Å2
Baniso -1Baniso -2Baniso -3
1--13.72 Å20 Å25.24 Å2
2--13.24 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 0 86 6158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9868316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74925.368272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1871530
X-RAY DIFFRACTIONr_chiral_restr0.0970.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7064.0083062
X-RAY DIFFRACTIONr_mcbond_other2.7244.2983053
X-RAY DIFFRACTIONr_mcangle_it4.0566.0073824
X-RAY DIFFRACTIONr_mcangle_other4.2876.4443815
X-RAY DIFFRACTIONr_scbond_it3.1454.1433098
X-RAY DIFFRACTIONr_scbond_other2.6694.5853083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2636.7534471
X-RAY DIFFRACTIONr_long_range_B_refined6.76433.9127061
X-RAY DIFFRACTIONr_long_range_B_other6.74733.9227040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 91 -
Rwork0.247 1463 -
obs--88.2 %

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