[English] 日本語
Yorodumi
- PDB-4q3r: Crystal structure of Schistosoma mansoni arginase in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q3r
TitleCrystal structure of Schistosoma mansoni arginase in complex with inhibitor ABHDP
Components(Arginase) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / arginase-deacetylase fold / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


arginase / arginase activity / : / urea cycle / manganese ion binding / nucleus / cytosol
Similarity search - Function
Arginase / Ureohydrolase domain / 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
: / : / TRIETHYLENE GLYCOL / Chem-XA2 / Arginase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.169 Å
AuthorsHai, Y. / Edwards, J.E. / Van Zandt, M.C. / Hoffmann, K.F. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2014
Title: Crystal Structure of Schistosoma mansoni Arginase, a Potential Drug Target for the Treatment of Schistosomiasis.
Authors: Hai, Y. / Edwards, J.E. / Van Zandt, M.C. / Hoffmann, K.F. / Christianson, D.W.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arginase
B: Arginase
C: Arginase
D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,58438
Polymers169,1014
Non-polymers4,48334
Water11,295627
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,78833
Polymers126,8503
Non-polymers3,93830
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area13630 Å2
ΔGint-304 kcal/mol
Surface area36000 Å2
MethodPISA
2
B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,84236
Polymers126,8503
Non-polymers3,99233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area13800 Å2
ΔGint-425 kcal/mol
Surface area34880 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,28930
Polymers126,8023
Non-polymers3,48727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area12620 Å2
ΔGint-303 kcal/mol
Surface area35740 Å2
MethodPISA
4
D: Arginase
hetero molecules

D: Arginase
hetero molecules

D: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,83315
Polymers126,8023
Non-polymers2,03112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area6300 Å2
ΔGint-114 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.488, 177.488, 177.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-558-

HOH

31B-588-

HOH

41C-514-

HOH

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Arginase


Mass: 42283.293 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_059980 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WVP6, arginase
#2: Protein Arginase


Mass: 42267.293 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_059980 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WVP6, arginase

-
Non-polymers , 7 types, 661 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cs
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-XA2 / (R)-2-amino-6-borono-2-(1-(3,4-dichlorobenzyl)piperidin-4-yl)hexanoic acid


Mass: 434.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28BCl2N2O5
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN ...THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.15 M cesium chloride, 13% w/v PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2014 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.169→50 Å / Num. all: 98198 / Num. obs: 96529 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.169-2.2510.11.196290181.19692.5
2.25-2.3412.70.9563.191320.95693.6
2.34-2.4413.90.7393.994120.73997.1
2.44-2.5714.90.5485.697180.54899.5
2.57-2.7316.70.422897660.42299.9
2.73-2.9518.90.29313.397850.293100
2.95-3.2421.10.19822.498230.198100
3.24-3.7122.30.14229.798490.142100
3.71-4.6722.50.10238.299020.102100
4.67-5022.20.07740.8101240.077100

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q3P

4q3p


Resolution: 2.169→49.226 Å / SU ML: 0.2 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 4812 4.99 %RANDOM
Rwork0.1744 ---
obs0.176 96490 98.26 %-
all-96497 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 2.169→49.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10094 0 181 627 10902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810482
X-RAY DIFFRACTIONf_angle_d1.08414212
X-RAY DIFFRACTIONf_dihedral_angle_d14.5883947
X-RAY DIFFRACTIONf_chiral_restr0.0421631
X-RAY DIFFRACTIONf_plane_restr0.0051831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1695-2.19410.29431500.2492830X-RAY DIFFRACTION92
2.1941-2.220.27171460.23342862X-RAY DIFFRACTION93
2.22-2.2470.29321460.23062882X-RAY DIFFRACTION93
2.247-2.27550.28231470.22292877X-RAY DIFFRACTION94
2.2755-2.30540.25041560.20642847X-RAY DIFFRACTION93
2.3054-2.3370.22191460.20842970X-RAY DIFFRACTION95
2.337-2.37040.21671530.20022905X-RAY DIFFRACTION96
2.3704-2.40580.21291650.20363028X-RAY DIFFRACTION97
2.4058-2.44340.26161690.20523006X-RAY DIFFRACTION98
2.4434-2.48340.24641440.18373076X-RAY DIFFRACTION99
2.4834-2.52620.24151690.18893065X-RAY DIFFRACTION100
2.5262-2.57220.23731680.18313085X-RAY DIFFRACTION100
2.5722-2.62160.21671400.18543111X-RAY DIFFRACTION100
2.6216-2.67510.20341860.18273075X-RAY DIFFRACTION100
2.6751-2.73330.24551760.18463086X-RAY DIFFRACTION100
2.7333-2.79690.22161670.1813048X-RAY DIFFRACTION100
2.7969-2.86680.22581620.1813146X-RAY DIFFRACTION100
2.8668-2.94430.22331740.18853072X-RAY DIFFRACTION100
2.9443-3.0310.22371540.1873088X-RAY DIFFRACTION100
3.031-3.12880.24071340.18383162X-RAY DIFFRACTION100
3.1288-3.24060.22471740.17723108X-RAY DIFFRACTION100
3.2406-3.37030.21671640.18213092X-RAY DIFFRACTION100
3.3703-3.52360.2171570.17043109X-RAY DIFFRACTION100
3.5236-3.70940.18991770.16413135X-RAY DIFFRACTION100
3.7094-3.94170.15441560.15253118X-RAY DIFFRACTION100
3.9417-4.24590.16851580.14243134X-RAY DIFFRACTION100
4.2459-4.67280.15471700.12693161X-RAY DIFFRACTION100
4.6728-5.34830.17351510.14643150X-RAY DIFFRACTION100
5.3483-6.73560.19761720.16893169X-RAY DIFFRACTION100
6.7356-49.2390.17021810.17143281X-RAY DIFFRACTION100

+
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