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- PDB-3il0: The crystal structure of the aminopeptidase P,XAA-pro aminopeptid... -

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Basic information

Entry
Database: PDB / ID: 3il0
TitleThe crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus
ComponentsAminopeptidase P; XAA-pro aminopeptidaseXaa-Pro aminopeptidase
KeywordsHYDROLASE / aminopeptidase P / XAA-pro aminopeptidase / Structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Aminopeptidase / Manganese / Metal-binding
Function / homology
Function and homology information


aminopeptidase 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
Aminopeptidase P XAA-pro aminopeptidase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, R. / Hatzos, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the aminopeptidase P,XAA-pro aminopeptidase from Streptococcus thermophilus
Authors: Zhang, R. / Hatzos, C. / Cobb, G. / Joachimiak, A.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase P; XAA-pro aminopeptidase
B: Aminopeptidase P; XAA-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5954
Polymers30,4112
Non-polymers1842
Water1,15364
1
A: Aminopeptidase P; XAA-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2972
Polymers15,2051
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminopeptidase P; XAA-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2972
Polymers15,2051
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.303, 80.396, 100.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminopeptidase P; XAA-pro aminopeptidase / Xaa-Pro aminopeptidase


Mass: 15205.298 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: GI:55737699, pepP, stu1742 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5M2R3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 289 K
Details: 0.2M Calcium acetate hydrate, 20% w/v PEG 3350, 25% glycerol, temperature 289K

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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 315r / Detector: CCD / Date: Jun 17, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→62.87 Å / Num. all: 17595 / Num. obs: 17521 / % possible obs: 99.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 24.1
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.89 / Num. unique all: 1345 / % possible all: 99.63

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→62.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.671 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.224 / ESU R Free: 0.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23688 947 5.1 %RANDOM
Rwork0.20132 ---
obs0.20314 17521 99.58 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.023 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--1.4 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 12 64 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222145
X-RAY DIFFRACTIONr_bond_other_d0.0010.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9512895
X-RAY DIFFRACTIONr_angle_other_deg1.04133520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47124.286112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3921514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_mcbond_it1.2281.51270
X-RAY DIFFRACTIONr_mcbond_other0.2791.5518
X-RAY DIFFRACTIONr_mcangle_it2.30522053
X-RAY DIFFRACTIONr_scbond_it3.2843875
X-RAY DIFFRACTIONr_scangle_it5.3224.5842
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 77 -
Rwork0.276 1263 -
obs-1340 99.63 %
Refinement TLS params.Method: refined / Origin x: 32.884 Å / Origin y: 11.143 Å / Origin z: 12.337 Å
111213212223313233
T0.1434 Å2-0.0337 Å2-0.0105 Å2-0.2613 Å20.0236 Å2--0.0327 Å2
L1.2226 °2-0.8907 °2-0.1072 °2-1.5854 °2-0.2916 °2--0.5442 °2
S0.0262 Å °-0.2063 Å °-0.1428 Å °0.0147 Å °-0.0441 Å °0.1509 Å °0.0568 Å °-0.0134 Å °0.0179 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 30
2X-RAY DIFFRACTION1A31 - 60
3X-RAY DIFFRACTION1A61 - 90
4X-RAY DIFFRACTION1A91 - 110
5X-RAY DIFFRACTION1A111 - 126
6X-RAY DIFFRACTION1B-1 - 30
7X-RAY DIFFRACTION1B31 - 60
8X-RAY DIFFRACTION1B61 - 90
9X-RAY DIFFRACTION1B91 - 110
10X-RAY DIFFRACTION1B111 - 126

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