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- PDB-3e6e: Crystal structure of Alanine racemase from E.faecalis complex wit... -

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Basic information

Entry
Database: PDB / ID: 3e6e
TitleCrystal structure of Alanine racemase from E.faecalis complex with cycloserine
ComponentsAlanine racemase
KeywordsISOMERASE / alr / scp / Pyridoxal phosphate
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding
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
Chem-DCS / Alanine racemase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHwang, K.Y. / Priyadarshi, A. / Lee, E.H. / Sung, M.W.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Structural insights into the alanine racemase from Enterococcus faecalis.
Authors: Priyadarshi, A. / Lee, E.H. / Sung, M.W. / Nam, K.H. / Lee, W.H. / Kim, E.E. / Hwang, K.Y.
History
DepositionAug 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,1046
Polymers123,1043
Non-polymers1,0003
Water2,342130
1
A: Alanine racemase
C: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7364
Polymers82,0702
Non-polymers6662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-14 kcal/mol
Surface area26960 Å2
MethodPISA
2
B: Alanine racemase
hetero molecules

B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7364
Polymers82,0702
Non-polymers6662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7400 Å2
ΔGint-19 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.597, 156.186, 146.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Alanine racemase /


Mass: 41034.816 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: alr, EF_0849 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q837J0, alanine racemase
#2: Chemical ChemComp-DCS / D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE / D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE


Mass: 333.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H16N3O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG8k, ca(OAc)2, Hepes, SCP, cyclohexyl-methyl-beta-d-maltoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2005 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 38010 / Num. obs: 35274 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.102 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.84 / Num. unique all: 3209 / Rsym value: 0.314 / % possible all: 88.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E5P

3e5p


Resolution: 2.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 5 -RANDOM
Rwork0.21 ---
all0.22 38010 --
obs0.22 35274 92.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8637 0 66 130 8833
Refine LS restraintsType: c_bond_d / Dev ideal: 0.0083
LS refinement shellResolution: 2.5→50 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.26 2141 -
Rwork0.22 --
obs-35274 92.8 %

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