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- PDB-5ib9: Crystal structure of aminopeptidase equipped with PAD from Aneuri... -

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Basic information

Entry
Database: PDB / ID: 5ib9
TitleCrystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1
ComponentsAminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aminopeptidase Protease-associated domain Homo-dimerization Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


metalloexopeptidase activity / aminopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M28 family / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase ...Peptidase M28 family / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BES / Aminopeptidase
Similarity search - Component
Biological speciesAneurinibacillus sp. AM-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTagawa, R. / Nakano, H. / Watanabe, K.
CitationJournal: To Be Published
Title: Crystal structure of aminopeptidase
Authors: Tagawa, R. / Nakano, H. / Watanabe, K.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9918
Polymers45,2901
Non-polymers7017
Water10,629590
1
A: Aminopeptidase
hetero molecules

A: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98116
Polymers90,5792
Non-polymers1,40214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3770 Å2
ΔGint-295 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.180, 68.443, 76.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Aminopeptidase /


Mass: 45289.699 Da / Num. of mol.: 1 / Fragment: UNP residues 36-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aneurinibacillus sp. AM-1 (bacteria) / Strain: AM-1 / Gene: amp / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: A2V759
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN / Ubenimex


Mass: 308.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 5.8
Details: 13% PEG 6000, 0.2M Zinc acetate, 0.1M MES-NaOH, pH 5.8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 89717 / % possible obs: 93.4 % / Redundancy: 4.8 % / Net I/σ(I): 27.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EK9

2ek9


Resolution: 1.4→39.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.195 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22284 4444 5 %RANDOM
Rwork0.1787 ---
obs0.18085 85042 92.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 25.748 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.4→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 28 590 3737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223192
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2681.9684319
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59425.217138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8915545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0621515
X-RAY DIFFRACTIONr_chiral_restr0.1530.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212403
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_it1.4731.52038
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35323267
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.56831154
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9194.51052
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.403→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 286 -
Rwork0.356 5334 -
obs--79.97 %

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