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- PDB-1n51: Aminopeptidase P in complex with the inhibitor apstatin -

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Basic information

Entry
Database: PDB / ID: 1n51
TitleAminopeptidase P in complex with the inhibitor apstatin
Components
  • Xaa-Pro aminopeptidase
  • apstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMINOPEPTIDASE / PROLINE SPECIFIC / MANGANESE ENZYME / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
APSTATIN / : / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGraham, S.C. / Maher, M.J. / Lee, M.H. / Simmons, W.H. / Freeman, H.C. / Guss, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of Escherichia coli aminopeptidase P in complex with the inhibitor apstatin.
Authors: Graham, S.C. / Maher, M.J. / Simmons, W.H. / Freeman, H.C. / Guss, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.
History
DepositionNov 3, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3675
Polymers50,2032
Non-polymers1653
Water7,656425
1
A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules

A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules

A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules

A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,47020
Polymers200,8108
Non-polymers65912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
2
A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules

A: Xaa-Pro aminopeptidase
B: apstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,73510
Polymers100,4054
Non-polymers3306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area7260 Å2
ΔGint-43 kcal/mol
Surface area34640 Å2
MethodPISA
3
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)199,63616
Polymers198,9764
Non-polymers65912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)139.319, 139.319, 231.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2157-

HOH

21A-2427-

HOH

DetailsBiological assembly is a tetramer formed by the crystallographic operations: (X,Y,Z), (-Y+1/2,-X+1/2,-Z+1/2), (Y-1/2,X+1/2,-Z+1/2), (-X,1-Y,Z)

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Components

#1: Protein Xaa-Pro aminopeptidase / AMINOPEPTIDASE P


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: Protein/peptide apstatin


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 458.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others) / References: APSTATIN
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 5.02 Å3/Da / Density % sol: 75.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Magnesium Acetate, Sodium Cacodylate, MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.7 mg/mlprotein1drop
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH6.8
425 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 24, 2000 / 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: 2.2→99 Å / Num. all: 48993 / Num. obs: 55327 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 42.6 Å2 / Limit h max: 63 / Limit h min: 0 / Limit k max: 44 / Limit k min: 0 / Limit l max: 104 / Limit l min: 0 / Observed criterion F max: 3136609.46 / Observed criterion F min: 17.3 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.58
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.46 / Num. unique all: 4729 / % possible all: 83.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % possible obs: 97 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 96.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1AZ9

1az9
PDB Unreleased entry


Resolution: 2.3→19.9 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2403 4.9 %RANDOM
Rwork0.179 ---
all-50531 --
obs-48993 97 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 37.434 Å2 / ksol: 0.299544 e/Å3
Displacement parametersBiso max: 100.3 Å2 / Biso mean: 44.58 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å20 Å2
2--5.15 Å20 Å2
3----10.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 3 425 3960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.3273085.20.29156520.0196231596095.7
2.4-2.530.3012984.90.25257810.0176256607997.2
2.53-2.690.2593185.20.21557500.0156222606897.5
2.69-2.90.2382674.30.19758750.0156278614297.8
2.9-3.190.2213115.10.19158340.0136285614597.8
3.19-3.650.1930850.18558750.0116329618397.7
3.65-4.580.17530550.14858470.016372615296.5
4.58-19.90.1652884.60.15159760.016602626494.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.333 / Rfactor Rwork: 0.299 / Num. reflection Rwork: 5361

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