[English] 日本語
Yorodumi
- PDB-5zeh: Crystal structure of Entamoeba histolytica Arginase in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zeh
TitleCrystal structure of Entamoeba histolytica Arginase in complex with L- Ornithine at 2.35 A
ComponentsArginase
KeywordsHYDROLASE / Metalloenzyme / Inhibition
Function / homology
Function and homology information


arginase / arginase activity / : / urea cycle / manganese ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Arginase / Ureohydrolase domain / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L-ornithine / Arginase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsMalik, A. / Dalal, V. / Ankri, S. / Tomar, S.
CitationJournal: Febs J. / Year: 2019
Title: Structural insights into Entamoeba histolytica arginase and structure-based identification of novel non-amino acid based inhibitors as potential antiamoebic molecules.
Authors: Malik, A. / Dalal, V. / Ankri, S. / Tomar, S.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arginase
B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2009
Polymers69,6542
Non-polymers5467
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.605, 97.494, 133.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 293 / Label seq-ID: 17 - 309

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Arginase


Mass: 34826.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_152330 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: C4LSS0, arginase
#2: Chemical ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: 0.1M bistris propane (pH-9.3), 0.2M potassium thiocyanate, 21% Peg6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.35→78.68 Å / Num. obs: 22967 / % possible obs: 96.4 % / Redundancy: 5.1 % / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2102 / CC1/2: 0.67 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→78.68 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 37.066 / SU ML: 0.369 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1152 5 %RANDOM
Rwork0.21863 ---
obs0.22082 21808 95.77 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.678 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2---1.91 Å20 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.36→78.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 26 74 4669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194695
X-RAY DIFFRACTIONr_bond_other_d0.0020.024489
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9776340
X-RAY DIFFRACTIONr_angle_other_deg0.9423.00210491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47625.96198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71815864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.821512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02822
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_it0.3642.652364
X-RAY DIFFRACTIONr_mcbond_other0.3612.652364
X-RAY DIFFRACTIONr_mcangle_it0.6553.9642948
X-RAY DIFFRACTIONr_mcangle_other0.6563.9662949
X-RAY DIFFRACTIONr_scbond_it0.2612.6852331
X-RAY DIFFRACTIONr_scbond_other0.262.6852331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4784.013393
X-RAY DIFFRACTIONr_long_range_B_refined4.33631.8595226
X-RAY DIFFRACTIONr_long_range_B_other4.33631.8765227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19608 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.356→2.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 80 -
Rwork0.405 1514 -
obs--90.88 %
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)
11.98620.03410.01863.17760.08241.1166-0.0289-0.12780.05890.51370.05390.0388-0.0275-0.023-0.0250.11320.05740.03610.27380.00241.0137-0.7135.07-8.977
22.3713-0.0158-0.27814.15790.08121.1163-0.08720.0727-0.08530.1090.086-0.3021-0.02390.03370.00120.0072-0.0015-0.00320.2781-0.02630.983924.507-22.809-24.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 294
2X-RAY DIFFRACTION2B-1 - 294

+
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