[English] 日本語
Yorodumi
- PDB-7k4i: Human Arginase 1 in complex with compound 06. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k4i
TitleHuman Arginase 1 in complex with compound 06.
ComponentsArginase-1
KeywordsHYDROLASE/HYDROLASE inhibitor / Arginase / hydrolase / arginine / urea cycle / inhibitor / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / Chem-VUY / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPalte, R.L.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors.
Authors: Li, D. / Zhang, H. / Lyons, T.W. / Lu, M. / Achab, A. / Pu, Q. / Childers, M. / Mitcheltree, M.J. / Wang, J. / Martinot, T.A. / McMinn, S.E. / Sloman, D.L. / Palani, A. / Beard, A. / Nogle, ...Authors: Li, D. / Zhang, H. / Lyons, T.W. / Lu, M. / Achab, A. / Pu, Q. / Childers, M. / Mitcheltree, M.J. / Wang, J. / Martinot, T.A. / McMinn, S.E. / Sloman, D.L. / Palani, A. / Beard, A. / Nogle, L. / Gathiaka, S. / Sauri, J. / Kim, H.Y. / Adpressa, D. / Spacciapoli, P. / Miller, J.R. / Palte, R.L. / Lesburg, C.A. / Cumming, J. / Fischer, C.
History
DepositionSep 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Dec 8, 2021Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arginase-1
B: Arginase-1
C: Arginase-1
D: Arginase-1
E: Arginase-1
F: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,91124
Polymers208,6796
Non-polymers2,23218
Water14,628812
1
A: Arginase-1
B: Arginase-1
E: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,45612
Polymers104,3403
Non-polymers1,1169
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-15 kcal/mol
Surface area33410 Å2
MethodPISA
2
C: Arginase-1
D: Arginase-1
F: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,45612
Polymers104,3403
Non-polymers1,1169
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-17 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.700, 287.100, 67.150
Angle α, β, γ (deg.)90.000, 90.280, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Arginase-1 / Liver-type arginase / Type I arginase


Mass: 34779.879 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-VUY / 3-[(1~{S},2~{S},5~{R})-2-carboxy-6-thia-3-azabicyclo[3.2.0]heptan-1-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide


Mass: 262.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H17BNO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MMT (pH 7.0) 0.1 M ammonium formate, 16-22% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→71.78 Å / Num. obs: 125565 / % possible obs: 89.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.53 Å2 / CC1/2: 0.994 / Net I/σ(I): 8.6
Reflection shellResolution: 1.98→2.09 Å / Num. unique obs: 12199 / CC1/2: 0.758

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V7E

6v7e


Resolution: 1.98→71.78 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.85 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.253 6219 4.96 %RANDOM
Rwork0.225 ---
obs0.227 125269 89.2 %-
Displacement parametersBiso max: 130.64 Å2 / Biso mean: 26.75 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.2923 Å20 Å2-0.247 Å2
2---8.1793 Å20 Å2
3---6.8871 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 1.98→71.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14454 0 114 812 15380
Biso mean--22.89 26.78 -
Num. residues----1902
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5160SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes312HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2148HARMONIC5
X-RAY DIFFRACTIONt_it14862HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1974SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18250SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14862HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg20184HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion15.38
LS refinement shellResolution: 1.98→2.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2458 508 4.94 %
Rwork0.2225 9767 -
all0.2237 10275 -
obs--99.62 %

+
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