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- PDB-1vft: Crystal structure of L-cycloserine-bound form of alanine racemase... -

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Basic information

Entry
Database: PDB / ID: 1vft
TitleCrystal structure of L-cycloserine-bound form of alanine racemase from D-cycloserine-producing Streptomyces lavendulae
Componentsalanine racemase
KeywordsISOMERASE / TIM-barrel / Greek-key motief
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 speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNoda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.
Authors: Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Self-protection mechanism in D-cycloserine-producing streptomyces lavendulae: Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase. which are ...Title: Self-protection mechanism in D-cycloserine-producing streptomyces lavendulae: Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase. which are traget enyzmes of D-cycloserine
Authors: Noda, M. / Kawahara, Y. / Ichikawa, A. / Matoba, Y. / Matsuo, H. / Lee, D.G. / Kumagai, T. / Sugiyama, M.
History
DepositionApr 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8005
Polymers82,0982
Non-polymers7023
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-17 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.770, 63.540, 85.320
Angle α, β, γ (deg.)90.00, 118.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alanine racemase


Mass: 41049.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: alr / Plasmid: pET-alr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q65YW7, alanine racemase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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.: 2 / Source method: obtained synthetically / Formula: C11H16N3O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 30, 2003 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 34960 / Num. obs: 34960 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3133 / % possible all: 89.5

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VFH

1vfh


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1597 5 %RANDOM
Rwork0.197 ---
all0.23 34960 --
obs0.197 32082 90.6 %-
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 45 117 5849
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_mcbond_it3.471.5
X-RAY DIFFRACTIONx_mcangle_it5.142
X-RAY DIFFRACTIONx_scbond_it5.742
X-RAY DIFFRACTIONx_scangle_it8.192.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 235 5.4 %
Rwork0.299 4086 -
obs-4086 73.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.KCXTOPH19.SOL
X-RAY DIFFRACTION3PARAM.SCP2TOP.KCX
X-RAY DIFFRACTION4TOP.SCP2

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