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- PDB-5dyf: The crystal structure of Aminopeptidase N in complex with N-benzy... -

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Basic information

Entry
Database: PDB / ID: 5dyf
TitleThe crystal structure of Aminopeptidase N in complex with N-benzyl-1,2-diaminoethylphosphonic acid
ComponentsAminopeptidase N
Keywordshydrolase/hydrolase inhibitor / AminopeptidaseN / Inhibitor complex / N-benzyl-1 / 2-diaminoethylphosphonic acid / hydrolase-hydrolase inhibitor complex / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding
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 / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5HR / IMIDAZOLE / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsNocek, B. / Joachimiak, A. / Vassiliou, S. / Berlicki, L. / Mucha, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: The crystal structure of Aminopeptidase N in complex with N-benzyl-1,2-diaminoethylphosphonic acid
Authors: Nocek, B. / Joachimiak, A. / Vassiliou, S. / Berlicki, L. / Mucha, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_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_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)100,38418
Polymers98,6901
Non-polymers1,69417
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.644, 224.644, 57.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aminopeptidase N


Mass: 98690.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Strain: MC58 / Gene: pepN, NMB1416 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JYV4, membrane alanyl aminopeptidase

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Non-polymers , 6 types, 754 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-5HR / [(1R)-1-amino-2-(benzylamino)ethyl]phosphonic acid


Mass: 230.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O3P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.854→28.65 Å / Num. obs: 119960 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GTQ

2gtq


Resolution: 1.854→28.65 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 6037 5.03 %Random selection
Rwork0.1459 ---
obs0.1474 119960 94.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.854→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 0 95 737 7635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057105
X-RAY DIFFRACTIONf_angle_d0.9159663
X-RAY DIFFRACTIONf_dihedral_angle_d13.9612583
X-RAY DIFFRACTIONf_chiral_restr0.0341061
X-RAY DIFFRACTIONf_plane_restr0.0041262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8535-1.87460.2649850.21931767X-RAY DIFFRACTION30
1.8746-1.89670.24761090.22422081X-RAY DIFFRACTION36
1.8967-1.91980.26461390.22122531X-RAY DIFFRACTION43
1.9198-1.94410.26031340.21042750X-RAY DIFFRACTION47
1.9441-1.96970.19531510.20212871X-RAY DIFFRACTION49
1.9697-1.99660.23171450.19332959X-RAY DIFFRACTION50
1.9966-2.02510.2221400.17512921X-RAY DIFFRACTION50
2.0251-2.05540.19121590.17342938X-RAY DIFFRACTION50
2.0554-2.08750.19961610.16822904X-RAY DIFFRACTION50
2.0875-2.12170.18711360.16252945X-RAY DIFFRACTION50
2.1217-2.15830.19611390.15962961X-RAY DIFFRACTION50
2.1583-2.19750.18261680.1662883X-RAY DIFFRACTION50
2.1975-2.23970.16651540.16462953X-RAY DIFFRACTION50
2.2397-2.28540.19511470.1622935X-RAY DIFFRACTION50
2.2854-2.33510.16361520.16292951X-RAY DIFFRACTION50
2.3351-2.38940.18551690.16262973X-RAY DIFFRACTION51
2.3894-2.44910.19291500.16463071X-RAY DIFFRACTION52
2.4491-2.51530.17711940.15243356X-RAY DIFFRACTION57
2.5153-2.58930.19122020.15733639X-RAY DIFFRACTION63
2.5893-2.67280.18881900.15314226X-RAY DIFFRACTION71
2.6728-2.76830.15652560.15494698X-RAY DIFFRACTION80
2.7683-2.8790.21092650.16265223X-RAY DIFFRACTION89
2.879-3.00990.18632810.16085539X-RAY DIFFRACTION94
3.0099-3.16840.20673460.1545615X-RAY DIFFRACTION97
3.1684-3.36660.20062780.14055856X-RAY DIFFRACTION98
3.3666-3.62610.15473140.11355701X-RAY DIFFRACTION98
3.6261-3.99010.12963050.10755695X-RAY DIFFRACTION97
3.9901-4.56550.11863400.10295621X-RAY DIFFRACTION97
4.5655-5.74440.16452980.12985824X-RAY DIFFRACTION99
5.7444-28.65650.18943300.17735536X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1323-0.2056-0.38651.07230.47481.8018-0.0652-0.0297-0.07750.0501-0-0.12070.24960.22820.0370.18170.03490.04040.10850.03870.143928.6947-50.474-8.3706
20.3206-0.0656-0.03170.57750.12471.2432-0.04190.0185-0.0512-0.0095-0.02460.06330.2112-0.19340.04670.1793-0.04130.04010.1234-0.00560.13422.8302-47.9927-15.2997
31.9869-0.13270.20981.76920.1671.1175-0.0959-0.008-0.1138-0.1974-0.11070.62530.151-0.58340.1480.2814-0.1226-0.0410.4542-0.08130.3538-17.0927-50.033-36.2755
40.8271-0.1201-0.15391.33180.55121.54630.02960.10670.0213-0.1387-0.10220.1891-0.149-0.46770.04980.17380.0739-0.03250.2423-0.01760.219-11.6932-22.4453-25.0556
51.7237-0.1373-0.20811.4021-0.23722.2558-0.0117-0.03190.2016-0.05550.001-0.0926-0.07330.01720.01880.16390.01060.00180.0568-0.00050.16759.7545-17.7504-17.7358
62.1881-0.91310.91731.59960.03622.83280.01290.0977-0.0159-0.1318-0.0343-0.0539-0.16650.09350.04060.1703-0.01750.03440.07550.01820.132317.2872-28.7344-34.8558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 190 )
2X-RAY DIFFRACTION2chain 'A' and (resid 191 through 451 )
3X-RAY DIFFRACTION3chain 'A' and (resid 452 through 555 )
4X-RAY DIFFRACTION4chain 'A' and (resid 556 through 723 )
5X-RAY DIFFRACTION5chain 'A' and (resid 724 through 789 )
6X-RAY DIFFRACTION6chain 'A' and (resid 790 through 867 )

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