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- PDB-4zi6: Crystal structure of leucine aminopeptidase from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4zi6
TitleCrystal structure of leucine aminopeptidase from Helicobacter pylori
ComponentsCytosol aminopeptidase
KeywordsHYDROLASE / Leucyl aminopeptidase / Cytosol
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / leucyl aminopeptidase / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases ...Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Cytosol aminopeptidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsModak, J.K. / Roujeinikova, A.
CitationJournal: Biochimie / Year: 2016
Title: Structural basis for substrate specificity of Helicobacter pylori M17 aminopeptidase.
Authors: Modak, J.K. / Rut, W. / Wijeyewickrema, L.C. / Pike, R.N. / Drag, M. / Roujeinikova, A.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosol aminopeptidase
B: Cytosol aminopeptidase
C: Cytosol aminopeptidase
D: Cytosol aminopeptidase
E: Cytosol aminopeptidase
F: Cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,14030
Polymers330,8516
Non-polymers1,28924
Water38,6962148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24460 Å2
ΔGint-161 kcal/mol
Surface area96910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.310, 99.430, 99.680
Angle α, β, γ (deg.)75.260, 61.080, 82.040
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytosol aminopeptidase / Leucine aminopeptidase / LAP / Leucyl aminopeptidase


Mass: 55141.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: pepA, HP_0570 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O25294, leucyl aminopeptidase, bacterial leucyl aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2148 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM sodium formate, 11% PEG 3350, 5.6 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→96.142 Å / Num. all: 179957 / Num. obs: 179957 / % possible obs: 85.1 % / Redundancy: 1.7 % / Biso Wilson estimate: 17.08 Å2 / Rpim(I) all: 0.067 / Rrim(I) all: 0.095 / Rsym value: 0.067 / Net I/av σ(I): 10.34 / Net I/σ(I): 7.7 / Num. measured all: 310850
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.111.60.3152.437983238860.3150.3152.277.3
2.11-2.241.60.2383.336791230700.2380.2382.978.9
2.24-2.391.60.1864.136399221770.1860.1863.680.7
2.39-2.581.70.1395.636078213030.1390.1394.783.3
2.58-2.831.70.1067.334795204100.1060.1065.986.7
2.83-3.161.80.07210.433814192890.0720.0728.390.9
3.16-3.651.90.0471533063175320.0470.0471393.4
3.65-4.471.90.03518.428589148180.0350.03517.593.7
4.47-6.321.90.03318.221953114020.0330.03317.593.1
6.32-32.3971.90.03217.11138560700.0320.03218.590.7

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
Blu-IceGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.397 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 9024 5.02 %Random
Rwork0.1705 170882 --
obs0.1732 179906 85.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.08 Å2 / Biso mean: 20.4961 Å2 / Biso min: 4.42 Å2
Refinement stepCycle: final / Resolution: 2→32.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22304 0 42 2148 24494
Biso mean--20.46 26.94 -
Num. residues----2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722869
X-RAY DIFFRACTIONf_angle_d1.00530828
X-RAY DIFFRACTIONf_chiral_restr0.043579
X-RAY DIFFRACTIONf_plane_restr0.0043875
X-RAY DIFFRACTIONf_dihedral_angle_d13.1918560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.28882810.22655141542277
2.0227-2.04650.30642930.23065121541477
2.0465-2.07150.30242700.24075202547277
2.0715-2.09770.30752700.23065185545578
2.0977-2.12530.27682960.21125193548978
2.1253-2.15440.27652720.20915275554779
2.1544-2.18520.26192740.20075263553778
2.1852-2.21780.28322860.19355347563379
2.2178-2.25240.29752690.19995326559580
2.2524-2.28930.28442600.19395356561680
2.2893-2.32880.23632610.18685440570181
2.3288-2.37110.26463060.18935454576081
2.3711-2.41670.26842720.18125482575482
2.4167-2.4660.26082870.17655532581983
2.466-2.51960.242850.17445620590584
2.5196-2.57820.24452870.18295616590384
2.5782-2.64270.273180.17255713603185
2.6427-2.71410.24093070.17655747605486
2.7141-2.79390.25473340.17635837617188
2.7939-2.8840.25333050.17655923622889
2.884-2.98710.21773270.16776088641590
2.9871-3.10660.20353460.1666197654392
3.1066-3.24780.21793040.16446190649493
3.2478-3.41890.21853390.16316265660494
3.4189-3.63280.19783470.15976180652793
3.6328-3.91290.18973420.14386289663194
3.9129-4.30580.16973190.13356287660694
4.3058-4.9270.15863230.13046268659194
4.927-6.20040.19143100.15856255656593
6.2004-32.40090.18683340.16766090642491

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