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- PDB-6g8b: E. coli Aminopeptidase N solved by Native SAD from a dataset coll... -

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Basic information

Entry
Database: PDB / ID: 6g8b
TitleE. coli Aminopeptidase N solved by Native SAD from a dataset collected in 60 second with JUNGFRAU detector
ComponentsAminopeptidase N
KeywordsHYDROLASE / Native-SAD / JUNGFRAU / integrating detector
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 / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / 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-7MF / Aminopeptidase N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.374 Å
AuthorsLeonarski, F. / Olieric, V. / Redford, S. / Wang, M.
CitationJournal: Nat. Methods / Year: 2018
Title: Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector.
Authors: Leonarski, F. / Redford, S. / Mozzanica, A. / Lopez-Cuenca, C. / Panepucci, E. / Nass, K. / Ozerov, D. / Vera, L. / Olieric, V. / Buntschu, D. / Schneider, R. / Tinti, G. / Froejdh, E. / ...Authors: Leonarski, F. / Redford, S. / Mozzanica, A. / Lopez-Cuenca, C. / Panepucci, E. / Nass, K. / Ozerov, D. / Vera, L. / Olieric, V. / Buntschu, D. / Schneider, R. / Tinti, G. / Froejdh, E. / Diederichs, K. / Bunk, O. / Schmitt, B. / Wang, M.
History
DepositionApr 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0356
Polymers101,4411
Non-polymers5945
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area34270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.109, 122.109, 172.021
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: 101441.195 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 BL21(DE3) (bacteria) / References: UniProt: P04825, membrane alanyl aminopeptidase

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Non-polymers , 5 types, 622 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-7MF / [(7~{S})-1-bromanyl-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium


Mass: 349.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19BrNO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 3.65 Å3/Da / Density % sol: 66.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.8M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 2.0667 Å
DetectorType: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jun 23, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0667 Å / Relative weight: 1
ReflectionResolution: 2.37→49.787 Å / Num. obs: 108726 / % possible obs: 93.8 % / Redundancy: 14.2 % / CC1/2: 0.99 / Rrim(I) all: 0.062 / Net I/σ(I): 34.06
Reflection shellResolution: 2.37→2.52 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6.07 / Num. unique obs: 12294 / CC1/2: 0.97 / Rrim(I) all: 0.18 / % possible all: 65.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.374→49.786 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 5420 4.99 %
Rwork0.1594 --
obs0.1617 108601 93.69 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.374→49.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 31 617 7599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038168
X-RAY DIFFRACTIONf_angle_d0.5211252
X-RAY DIFFRACTIONf_dihedral_angle_d16.0063251
X-RAY DIFFRACTIONf_chiral_restr0.0551224
X-RAY DIFFRACTIONf_plane_restr0.0031514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3739-2.40090.3107850.26131590X-RAY DIFFRACTION44
2.4009-2.42910.31031230.23362311X-RAY DIFFRACTION62
2.4291-2.45880.23521310.20932530X-RAY DIFFRACTION69
2.4588-2.48990.28211370.18652716X-RAY DIFFRACTION73
2.4899-2.52270.23041580.17192954X-RAY DIFFRACTION81
2.5227-2.55720.22281710.17643268X-RAY DIFFRACTION89
2.5572-2.59370.26141880.16633554X-RAY DIFFRACTION96
2.5937-2.63250.23371860.16573615X-RAY DIFFRACTION99
2.6325-2.67360.21731970.1673683X-RAY DIFFRACTION100
2.6736-2.71740.22781960.16443691X-RAY DIFFRACTION100
2.7174-2.76430.231930.17073607X-RAY DIFFRACTION100
2.7643-2.81450.22871930.16453692X-RAY DIFFRACTION100
2.8145-2.86870.2511860.16253618X-RAY DIFFRACTION100
2.8687-2.92720.23561960.16023711X-RAY DIFFRACTION100
2.9272-2.99090.20211980.15293656X-RAY DIFFRACTION100
2.9909-3.06040.2381880.16193658X-RAY DIFFRACTION100
3.0604-3.13690.22891930.17313688X-RAY DIFFRACTION100
3.1369-3.22170.21631910.16433638X-RAY DIFFRACTION100
3.2217-3.31650.20911880.16473669X-RAY DIFFRACTION100
3.3165-3.42350.22571930.16783687X-RAY DIFFRACTION100
3.4235-3.54590.17871940.16543670X-RAY DIFFRACTION100
3.5459-3.68780.21211930.15053706X-RAY DIFFRACTION100
3.6878-3.85560.19931900.14363620X-RAY DIFFRACTION100
3.8556-4.05880.15831960.12613689X-RAY DIFFRACTION100
4.0588-4.31290.16321920.11653661X-RAY DIFFRACTION100
4.3129-4.64570.1351910.10853646X-RAY DIFFRACTION100
4.6457-5.11280.13831940.11863671X-RAY DIFFRACTION100
5.1128-5.85160.19451970.16053685X-RAY DIFFRACTION100
5.8516-7.36860.21111900.20473636X-RAY DIFFRACTION99
7.3686-49.79730.22511920.21743661X-RAY DIFFRACTION99

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