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- PDB-1wl6: Mg-substituted form of E. coli aminopeptidase P -

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Basic information

Entry
Database: PDB / ID: 1wl6
TitleMg-substituted form of E. coli aminopeptidase P
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 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 21, 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4428
Polymers49,7441
Non-polymers6987
Water10,791599
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)201,76932
Polymers198,9764
Non-polymers2,79328
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
MethodPQS
2
A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,88516
Polymers99,4882
Non-polymers1,39614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area7800 Å2
ΔGint-70 kcal/mol
Surface area34970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.733, 177.733, 96.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 606 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL


Mass: 458.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 599 / 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 growMethod: vapor diffusion, hanging drop / Details: TRIS, PEG 4000, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 24, 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→42.26 Å / Num. all: 56174 / Num. obs: 56174 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Net I/σ(I): 26.53
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 5.39 / % possible all: 64.2

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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 HETATOMS

Resolution: 2→42.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.169 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17336 1708 3 %RANDOM
Rwork0.14751 ---
obs0.14832 54464 92.44 %-
all-54464 --
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: 17.504 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 43 599 4141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223626
X-RAY DIFFRACTIONr_bond_other_d0.0010.023319
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9694897
X-RAY DIFFRACTIONr_angle_other_deg0.7973.0027631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76523.636187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20715615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0151534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
X-RAY DIFFRACTIONr_nbd_refined0.2070.2760
X-RAY DIFFRACTIONr_nbd_other0.1810.23396
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21745
X-RAY DIFFRACTIONr_nbtor_other0.0810.22183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.37122854
X-RAY DIFFRACTIONr_mcbond_other0.572898
X-RAY DIFFRACTIONr_mcangle_it2.69533525
X-RAY DIFFRACTIONr_scbond_it2.5321644
X-RAY DIFFRACTIONr_scangle_it3.87831372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 79 -
Rwork0.201 2599 -
obs--60.77 %
Refinement TLS params.Method: refined / Origin x: 64.905 Å / Origin y: 58.488 Å / Origin z: 49.775 Å
111213212223313233
T0.0097 Å20.0092 Å20.0066 Å2-0.035 Å2-0.0023 Å2--0.0292 Å2
L0.2427 °2-0.1656 °20.0548 °2-0.4484 °2-0.1019 °2--0.416 °2
S-0.0216 Å °0.0329 Å °-0.0046 Å °0.0076 Å °-0.0245 Å °0.0199 Å °0.0512 Å °0.0011 Å °0.046 Å °

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