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- PDB-4pu2: Crystal structure of Aminopeptidase N in complex with the phospho... -

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Basic information

Entry
Database: PDB / ID: 4pu2
TitleCrystal structure of Aminopeptidase N in complex with the phosphonic acid analogue of leucine L-(R)-LeuP
ComponentsAminopeptidase N
KeywordsHYDROLASE / APN / aminopeptidase N / L-(R)-LeuP / PSI-Biology / Structural Genomics / Midwest Center for Structural Genomics / MCSG / aminopeptidase
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
LEUCINE PHOSPHONIC ACID / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsNocek, B. / Vassiliou, S. / Berlicki, L. / Mulligan, R. / Mucha, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Aminopeptidase N in complex with the phosphonic acid analogue of leucine
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 11, 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_asym_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_asym_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_asym_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
Revision 1.4Oct 16, 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)99,58710
Polymers98,6901
Non-polymers8979
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.328, 224.328, 57.909
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 , 5 types, 299 molecules

#2: Chemical ChemComp-PLU / LEUCINE PHOSPHONIC ACID


Mass: 167.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO3P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M AMMONIUM SULFATE, pH 6.5, 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: Sep 30, 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: 2.1→29.9 Å / Num. all: 60514 / Num. obs: 60514 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.14 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
CCP4model building
PHENIX(phenix.refine: dev_1639)refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GTQ

2gtq


Resolution: 2.095→29.887 Å / SU ML: 0.22 / σ(F): 1.65 / σ(I): 2 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 4432 5.11 %RANDOM
Rwork0.1776 ---
obs0.1792 56082 87.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.095→29.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6830 0 48 290 7168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037021
X-RAY DIFFRACTIONf_angle_d0.7259528
X-RAY DIFFRACTIONf_dihedral_angle_d14.122558
X-RAY DIFFRACTIONf_chiral_restr0.0281044
X-RAY DIFFRACTIONf_plane_restr0.0031248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0946-2.11840.3528440.2612935X-RAY DIFFRACTION23
2.1184-2.14330.2673540.23781027X-RAY DIFFRACTION25
2.1433-2.16950.3309680.23891156X-RAY DIFFRACTION29
2.1695-2.19690.2091740.2361341X-RAY DIFFRACTION33
2.1969-2.22580.2672940.23451546X-RAY DIFFRACTION38
2.2258-2.25630.23411060.23961781X-RAY DIFFRACTION45
2.2563-2.28850.27231060.23381978X-RAY DIFFRACTION49
2.2885-2.32270.25431330.23032198X-RAY DIFFRACTION54
2.3227-2.35890.28041150.22662381X-RAY DIFFRACTION59
2.3589-2.39760.2606980.22122429X-RAY DIFFRACTION60
2.3976-2.43890.25161410.22052645X-RAY DIFFRACTION64
2.4389-2.48330.25671620.21322735X-RAY DIFFRACTION68
2.4833-2.5310.26011520.21962878X-RAY DIFFRACTION72
2.531-2.58260.26872020.21823027X-RAY DIFFRACTION76
2.5826-2.63880.21911320.21033215X-RAY DIFFRACTION78
2.6388-2.70010.24911800.21863320X-RAY DIFFRACTION82
2.7001-2.76760.23081810.21213306X-RAY DIFFRACTION82
2.7676-2.84230.24281960.21133371X-RAY DIFFRACTION84
2.8423-2.92590.2391730.20823352X-RAY DIFFRACTION84
2.9259-3.02030.23451830.1993401X-RAY DIFFRACTION84
3.0203-3.12810.23042080.18983391X-RAY DIFFRACTION85
3.1281-3.25320.24991940.18863427X-RAY DIFFRACTION85
3.2532-3.40110.20352020.17563386X-RAY DIFFRACTION84
3.4011-3.58010.17421930.15553407X-RAY DIFFRACTION85
3.5801-3.8040.18461650.14213451X-RAY DIFFRACTION85
3.804-4.0970.14521710.14183450X-RAY DIFFRACTION85
4.097-4.50810.15462070.12423421X-RAY DIFFRACTION85
4.5081-5.15750.15371770.12973409X-RAY DIFFRACTION85
5.1575-6.4870.20631460.1753505X-RAY DIFFRACTION85
6.487-29.88960.20251750.15873480X-RAY DIFFRACTION86
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)
10.70060.0127-0.23630.1590.24211.4252-0.0966-0.0817-0.07140.03880.0462-0.03930.28590.26550.05510.26050.04350.02990.18320.03150.213325.6474-49.136332.027
20.2681-0.00760.06940.44980.1811.1429-0.0580.0504-0.0187-0.0479-0.02740.14110.2167-0.25290.07410.2813-0.07720.02940.2335-0.01340.2396-3.3728-48.936915.2394
30.8158-0.1583-0.04110.7690.1561.07960.0060.03570.0984-0.0926-0.02070.0883-0.1545-0.37890.01860.21520.058-0.00380.268-0.02050.2726-10.7006-21.471214.552
40.9203-0.0267-0.19741.1861-0.35591.1771-0.0334-0.01960.17220.02560.01720.0542-0.0902-0.0461-0.02720.27580.00370.01060.16260.00740.265611.2938-19.542219.8563
50.8018-0.25550.33080.830.05561.14170.00440.06170.0441-0.1488-0.0488-0.1255-0.06850.09490.03480.2715-0.01380.03440.18160.02090.230117.4773-28.69423.9444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 219 )
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 555 )
3X-RAY DIFFRACTION3chain 'A' and (resid 556 through 736 )
4X-RAY DIFFRACTION4chain 'A' and (resid 737 through 789 )
5X-RAY DIFFRACTION5chain 'A' and (resid 790 through 867 )

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