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- PDB-3ovk: Crystal structure of an XXA-pro aminopeptidase from Streptococcus... -

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Basic information

Entry
Database: PDB / ID: 3ovk
TitleCrystal structure of an XXA-pro aminopeptidase from Streptococcus pyogenes
ComponentsAMINOPEPTIDASE P, Xaa-Pro dipeptidase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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, 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
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoachimiak, A. / Duke, N.E.C. / Volkart, L. / Clancy, S. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of an XXA-pro aminopeptidase from Streptococcus pyogenes
Authors: Joachimiak, A. / Duke, N.E.C. / Volkart, L. / Clancy, S. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMINOPEPTIDASE P, Xaa-Pro dipeptidase
B: AMINOPEPTIDASE P, Xaa-Pro dipeptidase
C: AMINOPEPTIDASE P, Xaa-Pro dipeptidase
D: AMINOPEPTIDASE P, Xaa-Pro dipeptidase


Theoretical massNumber of molelcules
Total (without water)58,8134
Polymers58,8134
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.086, 116.991, 49.447
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AMINOPEPTIDASE P, Xaa-Pro dipeptidase


Mass: 14703.319 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: M28_Spy1536, SPY_1824 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q48RL4, Xaa-Pro dipeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.20M ammonium sulfate, 0.10M tri-sodium citrate pH 5.6, 25% w/v PEG4000, cryoprotectant, inclusion of glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97962 / Wavelength: 0.97962 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2→58.52 Å / Num. obs: 32829 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 68.192
Reflection shellResolution: 2→2.02 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 14.9 / Rsym value: 0.136 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→58.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.875 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1663 5.1 %RANDOM
Rwork0.176 ---
obs0.18 32787 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.18 Å2
2---0.17 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2→58.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 0 355 4367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224068
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9765492
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26423.636176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18915728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6341528
X-RAY DIFFRACTIONr_chiral_restr0.1270.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022984
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2751.52548
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24924076
X-RAY DIFFRACTIONr_scbond_it3.48531520
X-RAY DIFFRACTIONr_scangle_it5.5564.51416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 115 -
Rwork0.178 2269 -
obs--98.35 %

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