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- PDB-13ld: Deuterated alanine racemase from Geobacillus stearothermophilus -

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Basic information

Entry
Database: PDB / ID: 13ld
TitleDeuterated alanine racemase from Geobacillus stearothermophilus
ComponentsAlanine racemase
KeywordsISOMERASE / deuterated / alanine racemase / 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 / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel
Similarity search - Domain/homology
ACETATE ION / Alanine racemase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus 10 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeber, L.B. / Kovalevsky, A.Y. / Mueser, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137008 United States
CitationJournal: To Be Published
Title: Structure of deuterated alanine racemase from Geobacillus stearothermophilus
Authors: Leber, L.B. / Kovalevsky, A.Y. / Mueser, T.C.
History
DepositionMay 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)175,5288
Polymers175,2924
Non-polymers2364
Water8,701483
1
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7644
Polymers87,6462
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-14 kcal/mol
Surface area27430 Å2
MethodPISA
2
C: Alanine racemase
hetero molecules

D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7644
Polymers87,6462
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area6870 Å2
ΔGint-15 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.444, 109.925, 90.183
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alanine racemase


Mass: 43823.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus 10 (bacteria)
Strain: Alr / Gene: alr, dal / Plasmid: pET23a / Details (production host): pJK131 / Production host: Escherichia coli (E. coli) / References: UniProt: P10724, alanine racemase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 16 mg/mL protein, 12.5% PEG 4000, 100 mM sodium acetate, 100 mM tris pH 8.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 1, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→27.81 Å / Num. obs: 138839 / % possible obs: 99.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 24.13 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.067 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4085 / CC1/2: 0.668 / Rpim(I) all: 0.357 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.81 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 6724 5.17 %
Rwork0.1644 --
obs0.1665 130075 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12173 0 16 483 12672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412595
X-RAY DIFFRACTIONf_angle_d1.22817133
X-RAY DIFFRACTIONf_dihedral_angle_d15.4394653
X-RAY DIFFRACTIONf_chiral_restr0.0841877
X-RAY DIFFRACTIONf_plane_restr0.0132228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30192080.25644085X-RAY DIFFRACTION100
1.92-1.940.3042220.25014103X-RAY DIFFRACTION100
1.94-1.970.30762780.2434079X-RAY DIFFRACTION100
1.97-1.990.28622250.23284138X-RAY DIFFRACTION100
1.99-2.020.22682530.22034043X-RAY DIFFRACTION100
2.02-2.050.28252460.21964128X-RAY DIFFRACTION100
2.05-2.080.25612340.20814135X-RAY DIFFRACTION100
2.08-2.110.28492010.20854124X-RAY DIFFRACTION100
2.11-2.140.26212330.20414152X-RAY DIFFRACTION100
2.14-2.170.2412330.19324098X-RAY DIFFRACTION100
2.17-2.210.23452340.1934100X-RAY DIFFRACTION100
2.21-2.250.23542270.19214137X-RAY DIFFRACTION100
2.25-2.30.25472050.19244100X-RAY DIFFRACTION100
2.3-2.340.21441740.17584173X-RAY DIFFRACTION99
2.34-2.390.21412110.17584071X-RAY DIFFRACTION99
2.39-2.450.22651770.17854135X-RAY DIFFRACTION98
2.45-2.510.23912170.17774051X-RAY DIFFRACTION99
2.51-2.580.24032580.17624067X-RAY DIFFRACTION99
2.58-2.650.21072050.17954114X-RAY DIFFRACTION99
2.65-2.740.20972090.17434143X-RAY DIFFRACTION99
2.74-2.840.21672530.17564089X-RAY DIFFRACTION100
2.84-2.950.2171980.17574149X-RAY DIFFRACTION100
2.95-3.090.20912570.16974124X-RAY DIFFRACTION100
3.09-3.250.21412380.16744125X-RAY DIFFRACTION100
3.25-3.450.21261910.15624219X-RAY DIFFRACTION100
3.45-3.720.16682310.13484132X-RAY DIFFRACTION100
3.72-4.090.14422570.1244098X-RAY DIFFRACTION100
4.09-4.680.13632130.1084160X-RAY DIFFRACTION100
4.68-5.890.15252100.12184212X-RAY DIFFRACTION100
5.89-27.810.18032260.16543867X-RAY DIFFRACTION92

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