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

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Basic information

Entry
Database: PDB / ID: 4pvb
TitleCrystal structure of Aminopeptidase N in complex with the phosphonic acid analogue of leucine (D-(S)-LeuP)
ComponentsAminopeptidase N
KeywordsHYDROLASE / APN / aminopeptidase N / D-(S)-LeuP / 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 / 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 / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
[(1S)-1-amino-3-methylbutyl]phosphonic acid / PHOSPHATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 (D-(S)-LeuP)
Authors: Nocek, B. / Vassiliou, S. / Mulligan, R. / Weglarz-Tomczak, E. / Berlicki, L. / Pawelczak, M. / Mucha, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 16, 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)99,4989
Polymers98,6901
Non-polymers8088
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.264, 224.264, 57.943
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, 359 molecules

#2: Chemical ChemComp-2WW / [(1S)-1-amino-3-methylbutyl]phosphonic acid


Mass: 167.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO3P
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.84 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→32.39 Å / Num. all: 62983 / Num. obs: 61031 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.14 Å / % possible all: 98.1

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Processing

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

2gtq


Resolution: 2.1→32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.605 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.227 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23256 2753 5.1 %RANDOM
Rwork0.17673 ---
obs0.17953 51398 85.87 %-
all-54145 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.47 Å20 Å2
2--0.47 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6859 0 41 351 7251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197056
X-RAY DIFFRACTIONr_bond_other_d0.0020.026630
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9659565
X-RAY DIFFRACTIONr_angle_other_deg0.8483.00115227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39224.205352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.888151127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9491549
X-RAY DIFFRACTIONr_chiral_restr0.1080.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021663
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: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 105 -
Rwork0.21 2056 -
obs--46.44 %
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)
10.42970.06530.09960.38660.56581.3359-0.13360.0316-0.0174-0.05390.07730.0262-0.22760.24150.05630.1144-0.0502-0.04420.04850.0050.065132.539154.962914.0421
20.17970.05880.10320.02010.01770.7213-0.05940.0267-0.0455-0.01560.0013-0.0163-0.15130.05640.0580.1049-0.002-0.03580.031-0.0080.096923.574847.58483.2865
30.2057-0.1564-0.08480.2393-0.07960.4405-0.04050.0399-0.01760.0059-0.0052-0.0429-0.0475-0.13630.04570.07940.0269-0.02250.0493-0.01890.10155.142440.36024.069
40.08420.133-0.02970.25430.03320.6877-0.0314-0.0199-0.0211-0.0194-0.028-0.0327-0.1628-0.14520.05930.12340.0834-0.03730.0597-0.02690.07692.430952.086221.8607
52.32980.29530.34220.26270.24240.4043-0.0162-0.0554-0.01020.0722-0.08850.0568-0.0991-0.23720.10470.18270.1306-0.01930.1959-0.06830.0631-16.647852.200837.2781
60.19410.2424-0.27450.9154-0.21970.4430.03190.141-0.03420.0524-0.14530.0914-0.0134-0.31520.11340.0899-0.01160.04620.3625-0.14770.0805-18.057130.81333.3925
72.47781.12531.21080.91250.7731.828-0.0834-0.0057-0.03770.14710.0006-0.02810.0381-0.17250.08280.1015-0.02020.01150.0774-0.04690.0784-4.107424.907737.3609
80.72220.1795-0.15060.130.08030.2719-0.03450.1067-0.01530.0338-0.06110.02320.0738-0.2620.09560.0841-0.06730.00410.2636-0.07850.1061-14.471718.860815.5867
90.0782-0.04870.10410.5738-0.06290.4302-0.02990.0106-0.06840.01530.004-0.00510.0042-0.05530.02590.0676-0.02720.00790.022-0.02820.13795.709216.5816.0338
100.62270.502-0.20590.47920.05770.8121-0.0025-0.00720.02310.0345-0.01180.01160.05830.01190.01430.0730.0094-0.01440.02180.00270.116216.755628.495234.2369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 76
2X-RAY DIFFRACTION2A77 - 205
3X-RAY DIFFRACTION3A206 - 292
4X-RAY DIFFRACTION4A293 - 440
5X-RAY DIFFRACTION5A441 - 535
6X-RAY DIFFRACTION6A536 - 612
7X-RAY DIFFRACTION7A613 - 644
8X-RAY DIFFRACTION8A645 - 699
9X-RAY DIFFRACTION9A700 - 783
10X-RAY DIFFRACTION10A784 - 867

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