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- PDB-1xfc: The 1.9 A crystal structure of alanine racemase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 1xfc
TitleThe 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site
ComponentsAlanine racemase
KeywordsISOMERASE / alpha-beta barrel / beta-structure for c-terminal domain / internal aldimine form
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 / 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
PYRIDOXAL-5'-PHOSPHATE / Alanine racemase / Alanine racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsLeMagueres, P. / Im, H. / Ebalunode, J. / Strych, U. / Benedik, M.J. / Briggs, J.M. / Kohn, H. / Krause, K.L.
Citation
Journal: Biochemistry / Year: 2005
Title: The 1.9 A crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site.
Authors: LeMagueres, P. / Im, H. / Ebalunode, J. / Strych, U. / Benedik, M.J. / Briggs, J.M. / Kohn, H. / Krause, K.L.
#1: 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: Le Magueres, P. / Im, H. / Dvorak, A. / Strych, U. / Benedik, M. / Krause, K.L.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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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)82,0314
Polymers81,5372
Non-polymers4942
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-12 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.780, 164.780, 57.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

21A-482-

HOH

31B-493-

HOH

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Components

#1: Protein Alanine racemase /


Mass: 40768.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: alr / Plasmid: pMB1909 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0A4X2, UniProt: P9WQA9*PLUS, alanine racemase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: Sodium carbonate/bicarbonate, CaCl2, PEG400, HEPES, pH 9.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F110.916
SYNCHROTRONCHESS F120.9788, 0.9790, 0.9562, 0.9809
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 30, 2002
ADSC QUANTUM 42CCDJun 30, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
10.9 polarizationSINGLE WAVELENGTHMx-ray1
20.95 polarizationMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9161
20.97881
30.9791
40.95621
50.98091
ReflectionResolution: 1.8→30 Å / Num. all: 73618 / Num. obs: 67592 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Redundancy: 11.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6985 / % possible all: 95.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.254 1747 random
Rwork0.204 --
obs0.214 56748 -
all-63019 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 30 350 5740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d1.9

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