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- PDB-4zla: Bestatin complex structure of leucine aminopeptidase from Helicob... -

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Basic information

Entry
Database: PDB / ID: 4zla
TitleBestatin complex structure of leucine aminopeptidase from Helicobacter pylori
ComponentsCytosol aminopeptidase
KeywordsHYDROLASE/HYDROLASE inhibitor / Leucine aminopeptidase / Cytosol / hydrolase / bestatin / HYDROLASE-HYDROLASE inhibitor complex
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 / Chem-BES / Cytosol aminopeptidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Sep 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / 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)333,99036
Polymers330,8516
Non-polymers3,13930
Water42,9662385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24550 Å2
ΔGint-157 kcal/mol
Surface area97410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.770, 99.690, 96.780
Angle α, β, γ (deg.)81.890, 60.970, 75.390
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 5 types, 2415 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2385 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6% PEG 2K, 50 mM sodium formate, 5.6 mg/ml protein, 1 mM bestatin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→96.443 Å / Num. all: 230129 / Num. obs: 230129 / % possible obs: 92.6 % / Redundancy: 1.7 % / Biso Wilson estimate: 14.19 Å2 / Rpim(I) all: 0.069 / Rrim(I) all: 0.097 / Rsym value: 0.069 / Net I/av σ(I): 9.672 / Net I/σ(I): 7.9 / Num. measured all: 394571
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
1.9-21.70.3022.355259329670.3020.3022.690.8
2-2.121.70.216353770317160.2160.2163.692.2
2.12-2.271.70.1613.651515303770.1610.1614.794.1
2.27-2.451.70.1246.348270283660.1240.1245.794.5
2.45-2.691.70.0957.944755261840.0950.0957.194.4
2.69-31.70.06611.640342233870.0660.0669.193.9
3-3.471.70.04317.135679205270.0430.04312.793
3.47-4.251.80.02923.330045170830.0290.02917.191.8
4.25-6.011.80.02525.722973128670.0250.02518.889.6
6.01-30.5521.80.02719.21196366550.0270.02719.284.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
Blu-IceGUIdata collection
PHASERphasing
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H8G

3h8g


Resolution: 1.9→30.552 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 11550 5.02 %Random
Rwork0.1758 218484 --
obs0.178 230034 92.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.34 Å2 / Biso mean: 18.3288 Å2 / Biso min: 2.95 Å2
Refinement stepCycle: final / Resolution: 1.9→30.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22376 0 174 2385 24935
Biso mean--18.02 24.86 -
Num. residues----2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823040
X-RAY DIFFRACTIONf_angle_d1.01831047
X-RAY DIFFRACTIONf_chiral_restr0.0423601
X-RAY DIFFRACTIONf_plane_restr0.0053904
X-RAY DIFFRACTIONf_dihedral_angle_d12.7418579
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 (%)
1.9-1.92160.30243620.25117099746190
1.9216-1.94420.30533790.24027076745591
1.9442-1.96790.27443470.22997232757991
1.9679-1.99280.28574110.21517148755991
1.9928-2.0190.25953760.21247138751491
2.019-2.04670.27143930.20877175756892
2.0467-2.07590.26144020.217274767692
2.0759-2.10690.23533730.20297292766593
2.1069-2.13980.254140.19767279769393
2.1398-2.17490.22843650.18497438780394
2.1749-2.21240.2464220.18127390781294
2.2124-2.25260.24454110.19057414782594
2.2526-2.29590.23263920.18697430782295
2.2959-2.34270.23443710.17667374774594
2.3427-2.39370.2473870.18917501788895
2.3937-2.44930.23643700.17927458782895
2.4493-2.51050.22523790.17247432781194
2.5105-2.57840.22893950.187440783595
2.5784-2.65420.22043830.17087449783294
2.6542-2.73980.2113950.17017407780294
2.7398-2.83770.22723870.17917433782094
2.8377-2.95120.22664090.17127342775194
2.9512-3.08540.22233750.16697345772093
3.0854-3.24790.21083630.16567354771793
3.2479-3.45110.24010.16267296769793
3.4511-3.71720.19453830.16177274765792
3.7172-4.09050.18523900.1497144753492
4.0905-4.68060.16353590.13847146750590
4.6806-5.89010.18193960.15097001739789
5.8901-30.55630.17823600.16966703706385

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