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- PDB-5yq2: Crystal structure of E.coli aminopeptidase N in complex with Puro... -

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Basic information

Entry
Database: PDB / ID: 5yq2
TitleCrystal structure of E.coli aminopeptidase N in complex with Puromycin aminonucleoside
ComponentsAminopeptidase N
KeywordsHYDROLASE / O-Methyl-L-tyrosine / M1 class Aminopeptidase
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Peptidase M1, alanyl aminopeptidase, C-terminal domain / 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 fold ...Peptidase M1, alanyl aminopeptidase, C-terminal domain / 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 fold / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-GMC / MALONATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMarapaka, A.K. / Ganji, R.J. / Reddi, R. / Addlagatta, A.
CitationJournal: To Be Published
Title: Crystal structure of E.coli aminopeptidase N in complex with Puromycin aminonucleoside
Authors: Marapaka, A.K. / Ganji, R.J. / Reddi, R. / Addlagatta, A.
History
DepositionNov 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0797
Polymers101,3311
Non-polymers7486
Water14,520806
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-33 kcal/mol
Surface area33030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.223, 120.223, 170.124
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminopeptidase N / Alpha-aminoacylpeptide hydrolase


Mass: 101331.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pepN, b0932, JW0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P04825, membrane alanyl aminopeptidase

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Non-polymers , 5 types, 812 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GMC / (2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL / 6N-DIMETHYL-3'-DEOXY-AMINO-ADENOSINE


Mass: 294.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N6O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0M Sodium malonate / PH range: 7.2-7.6

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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: Oct 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 186872 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Χ2: 1.063 / Net I/σ(I): 19.6 / Num. measured all: 1040498
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.665.40.324185350.940.1520.3581.016100
1.66-1.725.50.246185510.9630.1150.2721.097100
1.72-1.85.50.188185030.9780.0870.2071.095100
1.8-1.95.60.138186010.9810.0640.1521.083100
1.9-2.025.70.101185900.990.0460.1111.095100
2.02-2.175.70.073186130.9930.0330.0811.008100
2.17-2.395.80.059186670.9910.0270.0651.009100
2.39-2.745.80.049187400.9970.0220.0531.068100
2.74-3.455.60.038188480.9980.0180.0421.076100
3.45-5050.03192240.9980.0150.0341.0999.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.383
Highest resolutionLowest resolution
Rotation29.61 Å1.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZO2.3.1data collection
SCALEPACK2.2.0data scaling
MOLREP11.4.05; 02.04.2016phasing
PDB_EXTRACT3.22data extraction
Coot0.8.2model building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HPO

2hpo


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1991 / WRfactor Rwork: 0.174 / FOM work R set: 0.887 / SU B: 1.032 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0594 / SU Rfree: 0.0615 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 9525 5.1 %RANDOM
Rwork0.1567 ---
obs0.1579 176842 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.52 Å2 / Biso mean: 24.334 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 48 806 7794
Biso mean--40.31 32.63 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0197233
X-RAY DIFFRACTIONr_bond_other_d0.0020.026778
X-RAY DIFFRACTIONr_angle_refined_deg2.5091.9569847
X-RAY DIFFRACTIONr_angle_other_deg1.9613.00215578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15324.263373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.007151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6051554
X-RAY DIFFRACTIONr_chiral_restr0.170.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218321
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021722
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 645 -
Rwork0.213 13089 -
all-13734 -
obs--99.95 %

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