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- PDB-1vfh: Crystal structure of alanine racemase from D-cycloserine producin... -

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Basic information

Entry
Database: PDB / ID: 1vfh
TitleCrystal structure 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 / 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
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 13, 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: Derived calculations / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2962
Polymers41,0491
Non-polymers2471
Water1,33374
1
A: alanine racemase
hetero molecules

A: alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5934
Polymers82,0982
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6740 Å2
ΔGint-10 kcal/mol
Surface area25610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.980, 63.380, 85.950
Angle α, β, γ (deg.)90.00, 120.14, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, 1-z.

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Components

#1: Protein alanine racemase


Mass: 41049.160 Da / Num. of mol.: 1
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: May 22, 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→100 Å / Num. all: 24889 / Num. obs: 24889 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.092 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6953 / Rsym value: 0.475 / % possible all: 86.9

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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 1SFT

1sft


Resolution: 2→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
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1193 4.9 %RANDOM
Rwork0.197 ---
all0.21 24889 --
obs0.197 24532 92.6 %-
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 15 74 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_improper_angle_d0.63
X-RAY DIFFRACTIONx_mcbond_it2.331.5
X-RAY DIFFRACTIONx_mcangle_it3.612
X-RAY DIFFRACTIONx_scbond_it3.952
X-RAY DIFFRACTIONx_scangle_it5.962.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 200 5.4 %
Rwork0.346 3512 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.KCXTOPH19.SOL
X-RAY DIFFRACTION3PARAM.PLP2TOP.KCX
X-RAY DIFFRACTION4TOP.PLP

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