[English] 日本語
Yorodumi
- PDB-4zla: Bestatin complex structure of leucine aminopeptidase from Helicob... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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
#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2385 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more