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- PDB-3o5v: The Crystal Structure of the Creatinase/Prolidase N-terminal doma... -

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Basic information

Entry
Database: PDB / ID: 3o5v
TitleThe Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A
ComponentsX-PRO dipeptidase
KeywordsHYDROLASE / Creatinase / dipeptidase / N-terminal / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative / Creatinase domain
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / metal ion binding
Similarity search - Function
Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative XAA-PRO dipeptidase X-PRO dipeptidase
Similarity search - Component
Biological speciesStreptococcus pyogenes M1 GAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsStein, A.J. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A
Authors: Stein, A.J. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: X-PRO dipeptidase
B: X-PRO dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3115
Polymers30,0922
Non-polymers2203
Water3,045169
1
A: X-PRO dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2664
Polymers15,0461
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: X-PRO dipeptidase


Theoretical massNumber of molelcules
Total (without water)15,0461
Polymers15,0461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.439, 79.439, 88.823
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-175-

HOH

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Components

#1: Protein X-PRO dipeptidase / Xaa-Pro dipeptidase / Putative XAA-PRO dipeptidase


Mass: 15045.927 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes M1 GAS (bacteria)
Gene: M5005_Spy0423, pepQ, SPy_0513 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9A119, Xaa-Pro dipeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 17% PEG 10,0000, 0.1M Bis-Tris pH 5.5, 0.1M Ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 27878 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.057 / Χ2: 1.633 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.924.90.59327401.01100
1.92-1.994.90.36827621.012100
1.99-2.084.90.25327611.083100
2.08-2.194.90.17227471.126100
2.19-2.334.90.12328211.152100
2.33-2.514.90.08927541.23100
2.51-2.764.90.06428051.369100
2.76-3.164.80.05428151.91999.9
3.16-3.994.70.04928413.34399.9
3.99-504.40.03628323.32795.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→36.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.95 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1390 5 %RANDOM
Rwork0.192 ---
obs0.194 27772 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.393 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 13 169 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222135
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9452919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3955263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81724.673107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8515320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.144156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211670
X-RAY DIFFRACTIONr_mcbond_it0.671.51290
X-RAY DIFFRACTIONr_mcangle_it1.23722092
X-RAY DIFFRACTIONr_scbond_it1.7653845
X-RAY DIFFRACTIONr_scangle_it2.94.5821
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 105 -
Rwork0.284 1903 -
all-2008 -
obs--99.8 %

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