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- PDB-4xo4: Crystal Structure of E. coli Aminopeptidase N in complex with L-M... -

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Basic information

Entry
Database: PDB / ID: 4xo4
TitleCrystal Structure of E. coli Aminopeptidase N in complex with L-Methionine
ComponentsAminopeptidase N
KeywordsHYDROLASE
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
METHIONINE / MALONATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsAddlagatta, A. / Gumpena, R.
CitationJournal: To Be Published
Title: Crystal Structure of E. coli Aminopeptidase N in complex with L-Methionine
Authors: Addlagatta, A. / Gumpena, R.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,09116
Polymers99,0291
Non-polymers1,06215
Water13,763764
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33140 Å2
Unit cell
Length a, b, c (Å)120.509, 120.509, 170.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 99028.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pepN, b0932, JW0915 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04825, membrane alanyl aminopeptidase

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Non-polymers , 6 types, 779 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium malonate

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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: Jan 5, 2015
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 80115 / % possible obs: 95.9 % / Redundancy: 3.6 % / Rsym value: 0.096 / Net I/σ(I): 9.72
Reflection shellResolution: 2.18→2.23 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HPO

2hpo


Resolution: 2.18→19.95 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.39 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16963 3718 5 %RANDOM
Rwork0.132 ---
obs0.13389 70334 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.692 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.18→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6973 0 61 764 7798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197273
X-RAY DIFFRACTIONr_bond_other_d0.0030.026848
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9549882
X-RAY DIFFRACTIONr_angle_other_deg1.043315715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68824.194372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.287151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4191555
X-RAY DIFFRACTIONr_chiral_restr0.1190.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021734
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_it2.2772.3873534
X-RAY DIFFRACTIONr_mcbond_other2.2722.3873532
X-RAY DIFFRACTIONr_mcangle_it3.2363.564423
X-RAY DIFFRACTIONr_mcangle_other3.2363.564424
X-RAY DIFFRACTIONr_scbond_it4.3562.9173739
X-RAY DIFFRACTIONr_scbond_other4.3482.9163737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7394.1625455
X-RAY DIFFRACTIONr_long_range_B_refined8.32420.4268751
X-RAY DIFFRACTIONr_long_range_B_other8.20619.98429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.182→2.238 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 241 -
Rwork0.159 4780 -
obs--93.34 %

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