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- PDB-1l6f: Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine -

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Basic information

Entry
Database: PDB / ID: 1l6f
TitleAlanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine
Componentsalanine racemase
KeywordsISOMERASE / alanine racemase / reaction mechanism / N-(5'-phosphopyridoxyl)-alanine
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
ALANYL-PYRIDOXAL-5'-PHOSPHATE / Alanine racemase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWatanabe, A. / Yoshimura, T. / Mikami, B. / Hayashi, H. / Kagamiyama, H. / Esaki, N.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.
Authors: Watanabe, A. / Yoshimura, T. / Mikami, B. / Hayashi, H. / Kagamiyama, H. / Esaki, N.
#1: Journal: Biochemistry / Year: 1997
Title: Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution
Authors: Shaw, J.P. / Petsko, G.A. / Ringe, D.
#2: Journal: Biochemistry / Year: 1998
Title: Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine
Authors: Stamper, G.F. / Morollo, A.A. / Ringe, D.
#3: Journal: Biochemistry / Year: 1999
Title: Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase
Authors: Morollo, A.A. / Petsko, G.A. / Ringe, D.
History
DepositionMar 9, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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)88,0314
Polymers87,3902
Non-polymers6402
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-12 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.960, 90.866, 85.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein alanine racemase


Mass: 43695.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pAR310 / Production host: Escherichia coli (E. coli) / References: UniProt: P10724, alanine racemase
#2: Chemical ChemComp-PP3 / ALANYL-PYRIDOXAL-5'-PHOSPHATE / PYRIDOXYL-ALANINE-5-PHOSPHATE / VITAMIN B6 COMPLEXED WITH ALANINE


Mass: 320.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG40001reservoir
2200 mMsodium acetate1reservoir
3100 mMTris-HCl1reservoirpH8.5
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 15, 1998 / Details: carbon monochrometer
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→43.1 Å / Num. all: 52427 / Num. obs: 52427 / % possible obs: 88.39 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 6.1 Å2 / Rsym value: 0.088 / Net I/σ(I): 1.48
Reflection shellResolution: 1.929→1.998 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 1.48 / Num. unique all: 2412 / Rsym value: 0.476 / % possible all: 73.2
Reflection
*PLUS
% possible obs: 88.4 % / Num. measured all: 199015 / Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFT

1sft


Resolution: 2→7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 493425.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4165 10.1 %RANDOM
Rwork0.172 ---
obs0.172 41051 79.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 116.24 Å2 / ksol: 0.486264 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å20 Å2
2---0.15 Å20 Å2
3----2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 42 292 6400
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it2.982
X-RAY DIFFRACTIONc_scbond_it3.352
X-RAY DIFFRACTIONc_scangle_it4.632.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 433 9.7 %
Rwork0.26 4048 -
obs-4481 52.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PLP.PARAMPLP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.88 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor obs: 0.26

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