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

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Basic information

Entry
Database: PDB / ID: 4oid
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 / Aspartic 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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 19, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)186,6784
Polymers186,6784
Non-polymers00
Water11,151619
1
A: Probable M18 family aminopeptidase 2
B: Probable M18 family aminopeptidase 2

A: Probable M18 family aminopeptidase 2
B: Probable M18 family aminopeptidase 2

A: Probable M18 family aminopeptidase 2
B: Probable M18 family aminopeptidase 2

C: Probable M18 family aminopeptidase 2
D: Probable M18 family aminopeptidase 2

C: Probable M18 family aminopeptidase 2
D: Probable M18 family aminopeptidase 2

C: Probable M18 family aminopeptidase 2
D: Probable M18 family aminopeptidase 2


Theoretical massNumber of molelcules
Total (without water)560,03312
Polymers560,03312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation7_544x+1/3,y-1/3,z-1/31
crystal symmetry operation8_654-y+4/3,x-y+2/3,z-1/31
crystal symmetry operation9_554-x+y+1/3,-x+2/3,z-1/31
Buried area80220 Å2
ΔGint-181 kcal/mol
Surface area152180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.606, 133.606, 320.959
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Probable M18 family aminopeptidase 2


Mass: 46669.410 Da / Num. of mol.: 4 / Mutation: D236A
Source method: isolated from a genetically manipulated source
Details: Cytosolic proteins / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: apeB, PA 3247, PA3247 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q9HYZ3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 295 K / pH: 8
Details: 30% PEG400, 0.1M Tris, 0.2M MgCl2, 0.1mM ZnCl2 , pH 8.0, Microbatch Crystallization, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.999999999
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2009
RadiationMonochromator: VARIABLE-INCLUDED-ANGLE PLANE- GRATING MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999999 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 94682 / % possible obs: 86 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 3.5 % / % possible all: 98.5

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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: 4NJQ

4njq


Resolution: 2.3→31.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.707 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20684 4678 5 %RANDOM
Rwork0.15718 ---
obs0.15969 88578 98.49 %-
all-4678 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.031 Å
Refinement stepCycle: LAST / Resolution: 2.3→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12609 0 0 619 13228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01912868
X-RAY DIFFRACTIONr_bond_other_d0.0020.028711
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.95417463
X-RAY DIFFRACTIONr_angle_other_deg1.105321028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.02151615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51423.106644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.947152022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.58615132
X-RAY DIFFRACTIONr_chiral_restr0.1350.21942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022763
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: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 341 -
Rwork0.177 6541 -
obs--99.16 %

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