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- PDB-4oiw: Structural and kinetic bases for the metal preference of the M18 ... -

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Basic information

Entry
Database: PDB / ID: 4oiw
TitleStructural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa
ComponentsProbable M18 family aminopeptidase 2
KeywordsHYDROLASE / Dodecameric TET structure / Aspartyl aminopeptidase / Pseudomonas aeruginosa / Histidine mutation / M18 family
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
M18 family aminopeptidase 2, putative / Aminopeptidase i, Domain 2 / Aminopeptidase i, Domain 2 / Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / Zn peptidases / Aminopeptidase / Roll / 3-Layer(aba) Sandwich ...M18 family aminopeptidase 2, putative / Aminopeptidase i, Domain 2 / Aminopeptidase i, Domain 2 / Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / Zn peptidases / Aminopeptidase / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable M18 family aminopeptidase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsNguyen, D.D. / Pandian, R. / Kim, D.D. / Ha, S.C. / Yoon, H.J. / Kim, K.S. / Yun, K.H. / Kim, J.H. / Kim, K.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa
Authors: Nguyen, D.D. / Pandian, R. / Kim, D. / Ha, S.C. / Yoon, H.J. / Kim, K.S. / Yun, K.H. / Kim, J.H. / Kim, K.K.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Sep 17, 2014Group: Database references
Revision 1.4Nov 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 / struct_ref_seq_dif / 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.ptnr2_auth_asym_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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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: Probable M18 family aminopeptidase 2
B: Probable M18 family aminopeptidase 2
C: Probable M18 family aminopeptidase 2
D: Probable M18 family aminopeptidase 2
E: Probable M18 family aminopeptidase 2
F: Probable M18 family aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,13512
Polymers280,7436
Non-polymers3926
Water16,033890
1
A: Probable M18 family aminopeptidase 2
B: Probable M18 family aminopeptidase 2
C: Probable M18 family aminopeptidase 2
D: Probable M18 family aminopeptidase 2
E: Probable M18 family aminopeptidase 2
F: Probable M18 family aminopeptidase 2
hetero molecules

A: Probable M18 family aminopeptidase 2
B: Probable M18 family aminopeptidase 2
C: Probable M18 family aminopeptidase 2
D: Probable M18 family aminopeptidase 2
E: Probable M18 family aminopeptidase 2
F: Probable M18 family aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,27124
Polymers561,48612
Non-polymers78512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area81350 Å2
ΔGint-654 kcal/mol
Surface area151760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.020, 218.267, 172.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Probable M18 family aminopeptidase 2


Mass: 46790.480 Da / Num. of mol.: 6 / Mutation: H82A
Source method: isolated from a genetically manipulated source
Details: 6 histag at the N-terminal / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: apeB, PA3247, Pseudomonas aeruginosa / Plasmid: pVFT1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q9HYZ3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 295 K / Method: microbatch crystallization / pH: 7.5
Details: 30%(v/v) 2-Propanol, 0.1M Hepes 7.5, 0.2M MgCl2, 10mM Spermidine, 0.1mM ZnCl2, microbatch Crystallization, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.7321 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 24, 2009
RadiationMonochromator: 0.17 2.3 keV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7321 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 95594 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.55→2.64 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NJR

4njr


Resolution: 2.44→48.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.104 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 5026 5 %RANDOM
Rwork0.14799 ---
obs0.15044 95594 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.364 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å20 Å20 Å2
2--2.53 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.44→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18936 0 6 890 19832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01919320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218372
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.95726232
X-RAY DIFFRACTIONr_angle_other_deg0.852341964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38752430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53423.168966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86153036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81715198
X-RAY DIFFRACTIONr_chiral_restr0.10.22922
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02122404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024698
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.442→2.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 266 -
Rwork0.216 4902 -
obs--67.07 %

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