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

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Basic information

Entry
Database: PDB / ID: 4njq
TitleStructural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa
ComponentsProbable M18 family aminopeptidase 2
KeywordsHYDROLASE / metallopeptidase / aspartyl aminopeptidase / cobalt complex / Tetrahedral shape dodecameric structure / Metal binding
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloaminopeptidase activity / proteolysis / zinc ion binding
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
: / CARBONATE ION / Probable M18 family aminopeptidase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsNguyen, D.D. / Pandian, R. / Kim, D.Y. / Ha, S.C. / Yun, K.H. / Kim, K.S. / 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
DepositionNov 11, 2013Deposition 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 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,18719
Polymers186,8544
Non-polymers1,33315
Water1,856103
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)564,56157
Polymers560,56112
Non-polymers4,00045
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area85630 Å2
ΔGint-474 kcal/mol
Surface area151170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.205, 133.205, 322.316
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: 46713.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N terminal 6 X His tag with TEV cutting site right after His tag
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: apeB, PA3247 / 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 295 K / Method: microbatch crystallization / pH: 8
Details: 30% PEG400, 0.2M magnesium chloride, 0.1mM zinc chloride , pH 8.0, Microbatch Crystallization, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270r / Detector: CCD / Date: Nov 7, 2013
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 54605 / Observed criterion σ(I): -3
Reflection shellResolution: 2.7→50 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.702→42.764 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU ML: 0.32 / σ(F): 1.97 / Phase error: 22.83 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.223 2920 5.08 %
Rwork0.1673 --
obs0.1702 54605 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.702→42.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12652 0 63 103 12818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812962
X-RAY DIFFRACTIONf_angle_d1.21117588
X-RAY DIFFRACTIONf_dihedral_angle_d16.7854732
X-RAY DIFFRACTIONf_chiral_restr0.0451954
X-RAY DIFFRACTIONf_plane_restr0.0052348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7024-2.74670.2691310.20152540X-RAY DIFFRACTION96
2.7467-2.7940.32961320.2112519X-RAY DIFFRACTION96
2.794-2.84480.26771330.19462558X-RAY DIFFRACTION96
2.8448-2.89950.27791470.1932521X-RAY DIFFRACTION97
2.8995-2.95870.28671460.18332586X-RAY DIFFRACTION97
2.9587-3.0230.2381650.17532564X-RAY DIFFRACTION98
3.023-3.09330.25251330.17622560X-RAY DIFFRACTION98
3.0933-3.17070.2581410.17952632X-RAY DIFFRACTION99
3.1707-3.25640.24091170.18532604X-RAY DIFFRACTION99
3.2564-3.35220.26531310.19152625X-RAY DIFFRACTION99
3.3522-3.46030.26851170.17732669X-RAY DIFFRACTION100
3.4603-3.58390.25251300.17662660X-RAY DIFFRACTION100
3.5839-3.72730.23381350.16362603X-RAY DIFFRACTION100
3.7273-3.89690.22021540.15482656X-RAY DIFFRACTION100
3.8969-4.10220.20011320.15052613X-RAY DIFFRACTION100
4.1022-4.35890.19511410.14492658X-RAY DIFFRACTION100
4.3589-4.69510.20621290.1372653X-RAY DIFFRACTION100
4.6951-5.16690.17511580.14772579X-RAY DIFFRACTION99
5.1669-5.91290.19871550.17042615X-RAY DIFFRACTION99
5.9129-7.44320.2221530.17732616X-RAY DIFFRACTION99
7.4432-42.76970.17841400.16972560X-RAY DIFFRACTION97

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