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- PDB-1rcq: The 1.45 A crystal structure of alanine racemase from a pathogeni... -

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Basic information

Entry
Database: PDB / ID: 1rcq
TitleThe 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms
Componentscatabolic alanine racemase DadX
KeywordsISOMERASE / alpha-beta barrel / beta-structure for c-terminal domain / internal/external aldimine forms
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / 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 / 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
D-LYSINE / PYRIDOXAL-5'-PHOSPHATE / Alanine racemase, catabolic
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsLe Magueres, P. / Im, H. / Dvorak, A. / Strych, U. / Benedik, M. / Krause, K.L.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.
Authors: LeMagueres, P. / Im, H. / Dvorak, A. / Strych, U. / Benedik, M. / Krause, K.L.
#1: Journal: Curr.Microbiol. / Year: 2000
Title: Characterization of the alanine racemases from Pseudomonas aeruginosa PAO1
Authors: Strych, U. / Huang, H.C. / Krause, K.L. / Benedik, M.J.
History
DepositionNov 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: catabolic alanine racemase DadX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5563
Polymers39,1631
Non-polymers3932
Water5,513306
1
A: catabolic alanine racemase DadX
hetero molecules

A: catabolic alanine racemase DadX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1136
Polymers78,3262
Non-polymers7874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6950 Å2
ΔGint-18 kcal/mol
Surface area25330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.679, 76.129, 136.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-511-

HOH

31A-706-

HOH

41A-728-

HOH

DetailsThe second monomer of the biological assembly is generated by a two-fold axis: x, -y+1, -z

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Components

#1: Protein catabolic alanine racemase DadX


Mass: 39162.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: dadx / Plasmid: pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HTQ2, 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: Chemical ChemComp-DLY / D-LYSINE


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 48.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 400, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9840, 0.9795, 0.9791, 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2000
RadiationMonochromator: 0.95 polarization / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
20.97951
30.97911
40.96111
ReflectionResolution: 1.45→99 Å / Num. all: 56981 / Num. obs: 56981 / % possible obs: 84.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 51.5
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1603 / % possible all: 36.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.45→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.206 2559 random
Rwork0.149 --
all0.153 54137 -
obs-49538 -
Displacement parametersBiso mean: 22.7 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 25 306 3084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d2.18

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