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- PDB-2rjh: Crystal structure of biosynthetic alaine racemase in D-cycloserin... -

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Basic information

Entry
Database: PDB / ID: 2rjh
TitleCrystal structure of biosynthetic alaine racemase in D-cycloserine-bound form from Escherichia coli
ComponentsAlanine racemase
KeywordsISOMERASE / alpha/beta barrel / Cell shape / Cell wall biogenesis/degradation / Isomerase / Peptidoglycan synthesis / Pyridoxal phosphate
Function / homologyAlanine racemase, N-terminal / Alanine racemase, C-terminal / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase, N-terminal domain / Alanine racemase, C-terminal domain / PLP-binding barrel / Alanine racemase / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase/group IV decarboxylase, C-terminal / D-alanine biosynthetic process ...Alanine racemase, N-terminal / Alanine racemase, C-terminal / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase, N-terminal domain / Alanine racemase, C-terminal domain / PLP-binding barrel / Alanine racemase / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase/group IV decarboxylase, C-terminal / D-alanine biosynthetic process / alanine racemase / alanine racemase activity / peptidoglycan biosynthetic process / cell wall organization / pyridoxal phosphate binding / regulation of cell shape / Alanine racemase, biosynthetic
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.4 Å resolution
AuthorsWu, D. / Hu, T. / Zhang, L. / Jiang, H. / Shen, X.
CitationJournal: Protein Sci. / Year: 2008
Title: Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis
Authors: Wu, D. / Hu, T. / Zhang, L. / Chen, J. / Du, J. / Ding, J. / Jiang, H. / Shen, X.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 15, 2007 / Release: Jul 8, 2008
RevisionDateData content typeGroupProviderType
1.0Jul 8, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion 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
C: Alanine racemase
D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,57414
Polyers165,6654
Non-polymers1,90910
Water10,196566
1
A: Alanine racemase
B: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8838
Polyers82,8322
Non-polymers1,0516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7640
ΔGint (kcal/M)-31.3
Surface area (Å2)26070
MethodPISA
2
C: Alanine racemase
D: Alanine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6916
Polyers82,8322
Non-polymers8594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7160
ΔGint (kcal/M)-18.7
Surface area (Å2)26090
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)147.713, 147.713, 163.724
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP 6

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Components

#1: Protein/peptide
Alanine racemase /


Mass: 41416.234 Da / Num. of mol.: 4 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: alr / Plasmid name: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6B4, alanine racemase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Formula: SO4 / Sulfate
#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.: 4 / Formula: C11H16N3O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Formula: H2O / Water

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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: 3.11 / Density percent sol: 60.48 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 1.6M ammonium sulfate, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Collection date: Nov 16, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.4 Å / D resolution low: 164.399 Å / Number obs: 78993 / Rmerge I obs: 0.121 / Rsym value: 0.121 / NetI over sigmaI: 6 / Redundancy: 9.7 % / Percent possible obs: 99.9
Reflection shell
Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured allNumber unique allRsym valueRedundancyPercent possible all
0.3952.402.531.988892114950.3957.7099.70
0.3212.532.682.393995109230.3218.60100.00
0.2602.682.872.992047101900.2609.00100.00
0.1882.873.104.09093895520.1889.50100.00
0.1263.103.395.98842087660.12610.10100.00
0.0863.393.798.68548679640.08610.70100.00
0.0673.794.3810.87903669980.06711.30100.00
0.0564.385.3712.76839159640.05611.50100.00
0.0675.377.5910.95299745880.06711.60100.00
0.0377.5940.9317.02868325530.03711.2099.30

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Processing

Software
NameVersionClassificationContact authorContact author emailLanguageLocationTypeDate
SCALAdata processingPhil Evanspre[at]mrc-lmb.cam.ac.ukFortran_77http://www.ccp4.ac.uk/dist/html/INDEX.htmlother
CNSrefinementAxel T. Brungeraxel.brunger[at]yale.eduFortran_77http://cns.csb.yale.edu/v1.1/package
PDB_EXTRACT3.000data extractionPDBsw-help[at]rcsb.rutgers.eduC++http://pdb.rutgers.edu/software/packageJuly 2, 2007
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RCQ
Details: This is a twinned structure, the detwin fraction is 0.400, and operator is 'h, -h-k, -l'.
Sigma F: 31
Solvent computationSolvent model param bsol: 37.124
Displacement parametersB iso mean: 20.374 Å2 / Aniso B11: -2.246 Å2 / Aniso B12: -3.529 Å2 / Aniso B13: 0 Å2 / Aniso B22: -2.246 Å2 / Aniso B23: 0 Å2 / Aniso B33: 4.492 Å2
Least-squares processR factor R free: 0.228 / R factor R work: 0.199 / Highest resolution: 2.4 Å / Lowest resolution: 15 Å / Number reflection R free: 7605 / Number reflection obs: 78640 / Percent reflection R free: 9.7 / Percent reflection obs: 99.9
Refine hist #LASTHighest resolution: 2.4 Å / Lowest resolution: 15 Å
Number of atoms included #LASTProtein: 10949 / Nucleic acid: 0 / Ligand: 118 / Solvent: 566 / Total: 11633
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1081.500
X-RAY DIFFRACTIONc_scbond_it1.7422.000
X-RAY DIFFRACTIONc_mcangle_it1.8192.000
X-RAY DIFFRACTIONc_scangle_it2.5742.500
Xplor file
Refine IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4kcx.param

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