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- PDB-5zi7: Crystal structure of Legionella pneumophila aminopeptidase A in c... -

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Basic information

Entry
Database: PDB / ID: 5zi7
TitleCrystal structure of Legionella pneumophila aminopeptidase A in complex with glutamic acid
ComponentsAminopeptidase N
KeywordsHYDROLASE / M1 class aminopeptidase
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like - #30 / Zincin-like ...Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Aminopeptidase N
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsMarapaka, A.K. / Addlagatta, A.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Discovery, Structural and Biochemical Studies of a rare Glu/Asp Specific M1 Class Aminopeptidase from Legionella pneumophila
Authors: Marapaka, A.K. / Pillalamarri, V. / Gumpena, R. / Haque, N. / Bala, S.C. / Jangam, A. / Addlagatta, A.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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
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: Aminopeptidase N
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,8064
Polymers209,5122
Non-polymers2942
Water16,268903
1
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9032
Polymers104,7561
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9032
Polymers104,7561
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.528, 103.749, 112.691
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminopeptidase N


Mass: 104756.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZVE3, membrane alanyl aminopeptidase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 903 / 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: 2.16 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M SPG, pH 6.0, 25 % PEG 1500 / PH range: 5.8-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→34.14 Å / Num. obs: 137053 / % possible obs: 99.2 % / Redundancy: 3 % / Biso Wilson estimate: 27.93 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.1
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 38086 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.559
Highest resolutionLowest resolution
Rotation34.14 Å2.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZO2.3.1data reduction
SCALEPACK2.2.0data scaling
MOLREP11.4.05; 02.04.2016phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HPO

2hpo


Resolution: 1.86→34.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.66 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.232 6926 5.1 %RANDOM
Rwork0.179 ---
obs0.182 129786 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13630 0 20 903 14553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914042
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213447
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.97419041
X-RAY DIFFRACTIONr_angle_other_deg1.056331050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30651738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27325.09668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95152543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2191566
X-RAY DIFFRACTIONr_chiral_restr0.1190.22146
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023134
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: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 442 -
Rwork0.299 9319 -
obs--95.77 %

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