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- PDB-4pw4: Crystal structure of Aminopeptidase N in complex with phosphonic ... -

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Basic information

Entry
Database: PDB / ID: 4pw4
TitleCrystal structure of Aminopeptidase N in complex with phosphonic acid analogue of homophenylalanine L-(R)-hPheP
ComponentsAminopeptidase N
KeywordsHYDROLASE/HYDROLASE INHIBITOR / APN / aminopeptidase N / complex with inhibitor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
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
[(1R)-1-amino-3-phenylpropyl]phosphonic acid / IMIDAZOLE / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNocek, B. / Mulligan, R. / Vassiliou, S. / Berlicki, L. / Mucha, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Aminopeptidase N in complex with phosphonic analogs of homophenylalanine
Authors: Nocek, B. / Vassiliou, S. / Mulligan, R. / Weglarz-Tomczak, E. / Berlicki, L. / Pawelczak, M. / Joachimiak, A. / Mucha, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Derived calculations / Structure summary / Category: audit_author / struct_conn
Item: _audit_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Sep 20, 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 / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)99,99714
Polymers98,6901
Non-polymers1,30613
Water14,304794
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.047, 224.047, 57.807
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 (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, 807 molecules

#2: Chemical ChemComp-2X0 / [(1R)-1-amino-3-phenylpropyl]phosphonic acid


Mass: 215.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14NO3P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: Jul 12, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→29.86 Å / Num. all: 91950 / Num. obs: 91950 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.88 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
CCP4model building
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GTQ

2gtq


Resolution: 1.85→29.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.736 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19298 4394 5 %RANDOM
Rwork0.1559 ---
obs0.1578 83245 95.05 %-
all-87639 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.29 Å20 Å2
2--0.29 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6852 0 71 794 7717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197104
X-RAY DIFFRACTIONr_bond_other_d0.0020.026671
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9699641
X-RAY DIFFRACTIONr_angle_other_deg0.9253.00115317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19624.148352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.987151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8311550
X-RAY DIFFRACTIONr_chiral_restr0.1320.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021683
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: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 222 -
Rwork0.201 4454 -
obs--68.77 %
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)
10.1690.07310.10230.31790.21360.5119-0.03810.0062-0.0293-0.0317-0.0028-0.015-0.09360.09080.04080.0419-0.0163-0.03430.02360.01330.058933.09154.0812-25.3247
20.14120.02310.0020.0183-0.0320.2398-0.0239-0.0023-0.0181-0.00970.003-0.013-0.0441-0.01980.02090.04290.0053-0.02270.0037-0.00340.065311.527844.871-33.4771
30.08810.0358-0.02730.0222-0.0380.4937-0.016-0.0208-0.02060.0155-0.0019-0.0209-0.1036-0.07110.01780.06610.0302-0.02560.0199-0.00390.0462.249352.9225-14.5588
40.52050.0080.11280.36650.10820.2683-0.09890.0283-0.03410.09320.0110.0684-0.1238-0.1040.08790.1280.0722-0.01070.0691-0.02740.0608-14.741752.1636-1.8645
50.31190.0826-0.04250.58460.0620.02480.05820.00210.04350.0727-0.07240.1163-0.0029-0.04350.01420.02350.00370.02910.128-0.0290.0565-18.103730.4724-5.5193
61.66210.4591.12990.60480.60431.7488-0.0020.05180.0480.1347-0.0463-0.00650.0271-0.09670.04830.0517-0.01630.00140.027-0.01590.052-2.565325.774-0.5047
70.46470.3148-0.35680.2186-0.27180.6706-0.04440.0430.0275-0.01730.03580.0120.004-0.21170.00860.0333-0.0041-0.00270.0904-0.01480.0712-14.46618.6769-21.599
80.42870.05530.50280.4183-0.05760.6545-0.0094-0.0467-0.08110.02480.0533-0.0355-0.0047-0.0989-0.04390.0393-0.0221-0.00940.0441-0.02090.1167-1.543713.5344-25.5374
90.0714-0.1093-0.01210.4173-0.10190.58660.00960.0018-0.0348-0.00430.00540.01330.01880.0014-0.0150.0354-0.0084-0.00820.00420.00550.078711.618719.3166-19.9999
100.23640.1919-0.08010.17770.03730.56340.0108-0.01140.020.0256-0.00860.01090.03940.0258-0.00220.038-0.0015-0.00930.00850.01090.068316.901228.6702-4.3758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 101
2X-RAY DIFFRACTION2A102 - 338
3X-RAY DIFFRACTION3A339 - 430
4X-RAY DIFFRACTION4A431 - 536
5X-RAY DIFFRACTION5A537 - 612
6X-RAY DIFFRACTION6A613 - 639
7X-RAY DIFFRACTION7A640 - 699
8X-RAY DIFFRACTION8A700 - 738
9X-RAY DIFFRACTION9A739 - 786
10X-RAY DIFFRACTION10A787 - 867

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