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- PDB-1wlr: Apo aminopeptidase P from E. coli -

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Basic information

Entry
Database: PDB / ID: 1wlr
TitleApo aminopeptidase P from E. coli
ComponentsXaa-Pro aminopeptidase
KeywordsHYDROLASE / Proline-specific peptidase / metalloenzyme / pita-bread fold
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, 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, methionine aminopeptidase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, 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, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsGraham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2005
Title: Structural and functional implications of metal ion selection in aminopeptidase p, a metalloprotease with a dinuclear metal center
Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
History
DepositionJun 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0945
Polymers49,7441
Non-polymers3504
Water8,215456
1
A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,37620
Polymers198,9764
Non-polymers1,39916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Unit cell
Length a, b, c (Å)177.322, 177.322, 96.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-877-

HOH

21A-1019-

HOH

DetailsThe biological assembly is a homotetramer generated by the operators: (x,y,z), (1-x,1-y,z), (y,x,4/3-z), (1-y,1-x,4/3-z)

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Components

#1: Protein Xaa-Pro aminopeptidase / X-Pro aminopeptidase / Aminopeptidase P II / APP-II / Aminoacylproline aminopeptidase


Mass: 49744.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pepP / Plasmid: pPL670 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: TRIS, PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 8, 1998 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 47221 / Num. obs: 47221 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Net I/σ(I): 32.93
Reflection shellResolution: 2.1→2.18 Å / Num. unique all: 2200 / Rsym value: 0.0717 / % possible all: 59.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Native aminopeptidase P without water, Mn or multiple conformers

Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.571 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17997 1475 3.1 %RANDOM
Rwork0.14939 ---
obs0.15036 45746 90.26 %-
all-45746 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 22 456 3977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223602
X-RAY DIFFRACTIONr_bond_other_d0.0030.023286
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9614871
X-RAY DIFFRACTIONr_angle_other_deg0.7953.0017588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69523.71186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13715613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9141533
X-RAY DIFFRACTIONr_chiral_restr0.0750.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
X-RAY DIFFRACTIONr_nbd_refined0.2040.2707
X-RAY DIFFRACTIONr_nbd_other0.1810.23346
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21731
X-RAY DIFFRACTIONr_nbtor_other0.0810.22159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.36522849
X-RAY DIFFRACTIONr_mcbond_other0.5682898
X-RAY DIFFRACTIONr_mcangle_it2.75233523
X-RAY DIFFRACTIONr_scbond_it2.65121622
X-RAY DIFFRACTIONr_scangle_it3.88431348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 70 -
Rwork0.169 2130 -
obs--58.22 %
Refinement TLS params.Method: refined / Origin x: 64.777 Å / Origin y: 58.321 Å / Origin z: 49.668 Å
111213212223313233
T0.0001 Å20.0139 Å20.0013 Å2-0.0304 Å2-0.0052 Å2--0.0207 Å2
L0.1475 °2-0.1094 °20.0474 °2-0.3565 °2-0.0872 °2--0.4155 °2
S-0.0232 Å °0.0269 Å °0.0032 Å °-0.0032 Å °-0.0176 Å °0.0144 Å °0.0411 Å °-0.0161 Å °0.0408 Å °

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