[English] 日本語
Yorodumi
- PDB-2aeb: Crystal structure of human arginase I at 1.29 A resolution and ex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aeb
TitleCrystal structure of human arginase I at 1.29 A resolution and exploration of inhibition in immune response.
ComponentsArginase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / BINUCLEAR MANGANESE CLUSTER / BORONIC ACID INHIBITOR / PERFECTLY TWINNED CRYSTAL / 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 / arginase activity / arginine catabolic process to ornithine / 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 / arginase activity / arginine catabolic process to ornithine / 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 / cytoplasm / cytosol
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
2(S)-AMINO-6-BORONOHEXANOIC ACID / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.29 Å
AuthorsDi Costanzo, L. / Sabio, G. / Mora, A. / Rodriguez, P.C. / Ochoa, A.C. / Centeno, F. / Christianson, D.W.
Citation
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.
#1: Journal: Biochemistry / Year: 2003
Title: Human arginase II: crystal structure and physiological role in male and female sexual arousal
Authors: Cama, E. / Colleluori, D.M. / Emig, F.A. / Shin, H. / Kim, S.W. / Kim, N.N. / Traish, A.M. / Ash, D.E. / Christianson, D.W.
#2: Journal: Nat.Struct.Biol. / Year: 1999
Title: Arginase-Boronic Acid Complex Highlights a Physiological Role in Erectile Function
Authors: Cox, J.D. / Kim, N.N. / Traish, A.M. / Christianson, D.W.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 27, 2011Group: Version format compliance
Revision 1.4Apr 3, 2013Group: Other
Revision 1.5Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.6Aug 23, 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 / struct_site
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)70,1648
Polymers69,5602
Non-polymers6046
Water6,918384
1
A: Arginase 1
hetero molecules

A: Arginase 1
hetero molecules

A: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24512
Polymers104,3403
Non-polymers9069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
B: Arginase 1
hetero molecules

B: Arginase 1
hetero molecules

B: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24512
Polymers104,3403
Non-polymers9069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)91.422, 91.422, 69.637
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-2518-

HOH

21B-1523-

HOH

-
Components

#1: Protein Arginase 1 / Liver-type arginase


Mass: 34779.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / 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-ABH / 2(S)-AMINO-6-BORONOHEXANOIC ACID


Mass: 191.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15BNO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.41 Å3/Da / Density % sol: 49.04 % / Description: DATA WERE SCALED AS SG P3.
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PegMME 5000, Bis Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K, pH 7.10

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 150499 / % possible obs: 92.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.6
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.85 / % possible all: 86

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1D3V

1d3v


Highest resolution: 1.29 Å
Details: DUE TO POORLY DEFINED DENSITY, THE FOLLOWING RESIDUES: A5, A48 (NZ), A222 (SIDE CHAINS), B41 (SIDE CHAINS), B48 (SIDE CHAINS), B89 (NZ), B222 (SIDE CHAINS) AND B224 (SIDE CHAINS) HAVE BEEN ...Details: DUE TO POORLY DEFINED DENSITY, THE FOLLOWING RESIDUES: A5, A48 (NZ), A222 (SIDE CHAINS), B41 (SIDE CHAINS), B48 (SIDE CHAINS), B89 (NZ), B222 (SIDE CHAINS) AND B224 (SIDE CHAINS) HAVE BEEN MODELED AT MINOR OCCUPANCY. BECAUSE PART OF A DISORDERED SIDE CHAINS, RESIDUES A83 AND B217 HAVE DISORDERED DENSITY. THEREFORE, HYDROGENS ARE NOT PLACED IN THE SIDECHAINS OF THESE TWO RESIDUE. REFINED TWIN FRACTIONS: 0.46. TWIN OPERATOR: -H, -K, L
RfactorNum. reflection
Rfree0.152 7526
all-150499
Refinement stepCycle: LAST / Highest resolution: 1.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 30 384 5145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.03
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d2.79
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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://pdbjlvh1.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