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- PDB-3h8e: Low pH native structure of leucine aminopeptidase from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 3h8e
TitleLow pH native structure of leucine aminopeptidase from Pseudomonas putida
ComponentsCytosol aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Cytoplasm / Manganese / Metal-binding / Protease
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases ...Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytosol aminopeptidase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å
AuthorsKale, A. / Dijkstra, B.W. / Sonke, T. / Thunnissen, A.M.W.H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the leucine aminopeptidase from Pseudomonas putida reveals the molecular basis for its enantioselectivity and broad substrate specificity.
Authors: Kale, A. / Pijning, T. / Sonke, T. / Dijkstra, B.W. / Thunnissen, A.M.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosol aminopeptidase
B: Cytosol aminopeptidase


Theoretical massNumber of molelcules
Total (without water)105,0632
Polymers105,0632
Non-polymers00
Water00
1
A: Cytosol aminopeptidase
B: Cytosol aminopeptidase

A: Cytosol aminopeptidase
B: Cytosol aminopeptidase

A: Cytosol aminopeptidase
B: Cytosol aminopeptidase


Theoretical massNumber of molelcules
Total (without water)315,1886
Polymers315,1886
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area18580 Å2
ΔGint-43 kcal/mol
Surface area102490 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-10 kcal/mol
Surface area38000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.946, 116.946, 137.899
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Cytosol aminopeptidase / Leucine aminopeptidase / LAP / Leucyl aminopeptidase


Mass: 52531.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: ATCC12633 / Gene: pepA / Plasmid: pTrpLAP / Production host: Escherichia coli (E. coli) / References: UniProt: O86436, leucyl aminopeptidase

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 11% (w/v) PEG 8000, 0.2 M Na formate, 0.1 M MES-NaOH, pH 5.2, 1 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 8.6 / Number: 111116 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / D res high: 2.75 Å / D res low: 101.535 Å / Num. obs: 27855 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.758.5299.510.0330.0333.9
6.158.710010.0380.0384
5.026.1510010.0450.0454
4.355.0210010.0450.0454
3.894.3510010.0550.0554
3.553.8910010.0750.0754
3.293.5510010.1130.1134
3.073.2910010.1620.1624
2.93.0710010.2420.2424
2.752.910010.3530.3533.9
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.75→101.535 Å / Num. all: 27831 / Num. obs: 27831 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.353 / Net I/σ(I): 15.4
Reflection shellResolution: 2.75→2.9 Å / % possible all: 99.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.75 Å58.47 Å
Translation2.75 Å58.47 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementResolution: 2.75→58 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.267 1313 4.7 %
Rwork0.212 26515 -
obs-27828 100 %
Solvent computationBsol: 32.163 Å2
Displacement parametersBiso max: 60.47 Å2 / Biso mean: 13.301 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-5.583 Å2-5.789 Å20 Å2
2--5.673 Å20 Å2
3----11.171 Å2
Refinement stepCycle: LAST / Resolution: 2.75→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 0 0 0 7006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.0161.5
X-RAY DIFFRACTIONc_scbond_it0.7631.5
X-RAY DIFFRACTIONc_mcangle_it1.7232
X-RAY DIFFRACTIONc_scangle_it1.4292.5
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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