[English] 日本語
Yorodumi
- PDB-4zw3: X-ray crystal structure of PfA-M1 in complex with hydroxamic acid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zw3
TitleX-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 9b
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE inhibitor / M1 ALANYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm
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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4S9 / PHOSPHATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDrinkwater, N. / McGowan, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1063786 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions.
Authors: Drinkwater, N. / Vinh, N.B. / Mistry, S.N. / Bamert, R.S. / Ruggeri, C. / Holleran, J.P. / Loganathan, S. / Paiardini, A. / Charman, S.A. / Powell, A.K. / Avery, V.M. / McGowan, S. / Scammells, P.J.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M1 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4757
Polymers103,7611
Non-polymers7146
Water15,565864
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.230, 109.340, 117.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 103760.719 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084 / Mutation: N213Q, N223Q, H378P, N501Q, N795Q, N1069Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate FcB1 / Columbia) (eukaryote)
Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

-
Non-polymers , 6 types, 870 molecules

#2: Chemical ChemComp-4S9 / tert-butyl [(1S)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]carbamate


Mass: 345.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17BrN2O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris pH 8.5, 0.2 M MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 3, 2014
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→80.11 Å / Num. obs: 89885 / % possible obs: 99.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.07 / Net I/σ(I): 9.8 / Num. measured all: 639057 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.8-1.836.82.0911.53085845120.4980.84998.1
9.69-80.116.40.05324.542986750.9960.02399.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.8data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBG

3ebg


Resolution: 1.8→44.226 Å / FOM work R set: 0.8774 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 4505 5.02 %
Rwork0.1597 85291 -
obs0.1616 89796 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.72 Å2 / Biso mean: 25.28 Å2 / Biso min: 8.5 Å2
Refinement stepCycle: final / Resolution: 1.8→44.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 39 864 8102
Biso mean--34.78 35.31 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077523
X-RAY DIFFRACTIONf_angle_d1.00810220
X-RAY DIFFRACTIONf_chiral_restr0.0411136
X-RAY DIFFRACTIONf_plane_restr0.0051302
X-RAY DIFFRACTIONf_dihedral_angle_d12.7792819
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 (%)
1.8-1.82050.3161170.28062817293498
1.8205-1.84190.3351360.26352820295698
1.8419-1.86430.28471440.25082793293799
1.8643-1.88790.26131470.2312769291698
1.8879-1.91280.29461350.22662815295099
1.9128-1.9390.26031660.21472750291698
1.939-1.96670.25391470.20342806295399
1.9667-1.9960.23851420.19232821296399
1.996-2.02720.23851410.18732792293399
2.0272-2.06050.22961740.17612797297199
2.0605-2.0960.21181550.16842787294298
2.096-2.13410.18541660.158728022968100
2.1341-2.17520.21741600.16432796295699
2.1752-2.21960.23061490.15752860300999
2.2196-2.26780.21561280.163528372965100
2.2678-2.32060.20751610.16192798295999
2.3206-2.37860.23191470.16672817296499
2.3786-2.44290.21991310.162864299599
2.4429-2.51480.21061620.16112836299899
2.5148-2.59590.18441610.159228382999100
2.5959-2.68870.19391410.157128653006100
2.6887-2.79630.22121570.164528443001100
2.7963-2.92360.20731620.158628413003100
2.9236-3.07770.19541540.160128683022100
3.0777-3.27050.20041450.15729093054100
3.2705-3.52290.18991310.143328973028100
3.5229-3.87720.14241550.13329193074100
3.8772-4.43780.14841500.125829273077100
4.4378-5.58940.15411580.12829383096100
5.5894-44.23890.1641830.155930683251100
Refinement TLS params.Method: refined / Origin x: 92.8414 Å / Origin y: 113.1908 Å / Origin z: 10.1275 Å
111213212223313233
T0.0892 Å20.0001 Å20.0149 Å2-0.1156 Å20.0135 Å2--0.1003 Å2
L0.4093 °2-0.1908 °20.0438 °2-0.9905 °20.2357 °2--0.7983 °2
S-0.0709 Å °-0.0302 Å °0.0386 Å °0.032 Å °0.027 Å °0.003 Å °-0.0754 Å °-0.0078 Å °0.0372 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 1084
2X-RAY DIFFRACTION1allA1
3X-RAY DIFFRACTION1allB1
4X-RAY DIFFRACTION1allD8 - 12
5X-RAY DIFFRACTION1allD1
6X-RAY DIFFRACTION1allC1 - 905
7X-RAY DIFFRACTION1allE1

+
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