[English] 日本語
Yorodumi
- PDB-3sjt: Crystal structure of human arginase I in complex with the inhibit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sjt
TitleCrystal structure of human arginase I in complex with the inhibitor Me-ABH, Resolution 1.60 A, twinned structure
ComponentsArginase-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / ABH inhibitor derivative / twinning / 2-Amino-6-borono-2-methylhexanoic acid / 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
Ureohydrolase domain / Arginase / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
[(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
Citation
Journal: J.Med.Chem. / Year: 2011
Title: Binding of alpha , alpha-disubstituted amino acids to arginase suggests new avenues for inhibitor design.
Authors: Ilies, M. / Di Costanzo, L. / Dowling, D.P. / Thorn, K.J. / Christianson, D.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response.
Authors: Di Costanzo, L. / Sabio, G. / Mora, A. / Rodriguez, P.C. / Ochoa, A.C. / Centeno, F. / Christianson, D.W.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Atomic model
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1928
Polymers69,5602
Non-polymers6326
Water13,781765
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28712
Polymers104,3403
Non-polymers9489
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5610 Å2
ΔGint-18 kcal/mol
Surface area32500 Å2
MethodPISA
2
B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28712
Polymers104,3403
Non-polymers9489
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5510 Å2
ΔGint-17 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.337, 90.337, 69.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-436-

HOH

31B-350-

HOH

41B-352-

HOH

51B-497-

HOH

-
Components

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


Mass: 34779.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pet-11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3) / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-5AB / [(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate


Type: L-peptide linking / Mass: 206.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17BNO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING MATERIAL 2-AMINO-6-BORONO-2-METHYLHEXANOIC ACID (MABH) UNDERGOES TO NUCLEOPHILIC ...THE STARTING MATERIAL 2-AMINO-6-BORONO-2-METHYLHEXANOIC ACID (MABH) UNDERGOES TO NUCLEOPHILIC ATTACK BY THE HYDROXYL GROUP BRIDING THE DI-MANGANESE CLUSTER OF THE ENZYME.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 3 uL of protein solution [3.5 mg/mL HAI, 50 mM bicine (pH 8.5), 2 mM MABH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 22-28% Jeffamine] were equilibrated against a ...Details: 3 uL of protein solution [3.5 mg/mL HAI, 50 mM bicine (pH 8.5), 2 mM MABH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 22-28% Jeffamine] were equilibrated against a 1 mL reservoir of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2008
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 1.597→50 Å / Num. obs: 82598 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.1
Reflection shellResolution: 1.597→1.7 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.7 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ZAV

2zav


Resolution: 1.597→34.068 Å / σ(F): 0.09 / Phase error: 17.86 / Stereochemistry target values: TWIN_LSQ_F / Details: twinning fraction = 0.5 twin law = -h, -k, l
RfactorNum. reflection% reflection
Rfree0.1631 2039 2.51 %
Rwork0.1292 --
obs0.1301 81125 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.135 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0703 Å2-0 Å2-0 Å2
2--1.0703 Å20 Å2
3----2.1405 Å2
Refinement stepCycle: LAST / Resolution: 1.597→34.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 32 765 5559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064888
X-RAY DIFFRACTIONf_angle_d1.046636
X-RAY DIFFRACTIONf_dihedral_angle_d17.5991828
X-RAY DIFFRACTIONf_chiral_restr0.066760
X-RAY DIFFRACTIONf_plane_restr0.005850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5985-1.63850.25181390.23955121526086
1.6385-1.68280.22461340.22635291542588
1.6828-1.73230.25941350.21665440557591
1.7323-1.78820.20541310.2075542567393
1.7882-1.85210.21941430.19095661580495
1.8521-1.92620.22661410.17565768590996
1.9262-2.01390.18241430.17665776591997
2.0139-2.120.1621540.15755823597797
2.12-2.25280.17851520.15255790594297
2.2528-2.42670.14521480.14455852600097
2.4267-2.67070.18671440.13585853599798
2.6707-3.05690.16611410.11785802594397
3.0569-3.850.13781390.0865765590496
3.85-29.57480.11371350.07555530566592

+
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