[English] 日本語
Yorodumi
- PDB-4r8k: Crystal structure of the guinea pig L-asparaginase 1 catalytic domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r8k
TitleCrystal structure of the guinea pig L-asparaginase 1 catalytic domain
ComponentsUncharacterized protein
KeywordsHYDROLASE / L-asparaginase
Function / homology
Function and homology information


: / asparaginase / asparaginase activity
Similarity search - Function
Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like ...Type I (cytosolic) L-asparaginase / L-asparaginase, N-terminal domain / Rossmann fold - #40 / L-asparaginase, C-terminal / Asparaginase/glutaminase, active site 2 / Asparaginase/glutaminase, C-terminal / Glutaminase/Asparaginase C-terminal domain / Asparaginase / glutaminase active site signature 2. / Asparaginase / Asparaginase/glutaminase-like / L-asparaginase, N-terminal / Asparaginase/glutaminase-like superfamily / L-asparaginase, N-terminal domain superfamily / Asparaginase, N-terminal / Asparaginase / glutaminase domain profile. / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchalk, A.M. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Identification and Structural Analysis of an l-Asparaginase Enzyme from Guinea Pig with Putative Tumor Cell Killing Properties.
Authors: Schalk, A.M. / Nguyen, H.A. / Rigouin, C. / Lavie, A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 10, 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 / struct_ncs_dom_lim / 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 / _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 / _struct_ref_seq_dif.details / _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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,72616
Polymers335,8198
Non-polymers1,9068
Water16,069892
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8638
Polymers167,9104
Non-polymers9534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-61 kcal/mol
Surface area50920 Å2
MethodPISA
2
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8638
Polymers167,9104
Non-polymers9534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-63 kcal/mol
Surface area50510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.550, 123.310, 120.560
Angle α, β, γ (deg.)90.00, 92.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA7 - 36130 - 384
21SERSERPROPROBB7 - 36130 - 384
12GLUGLULEULEUAA8 - 36031 - 383
22GLUGLULEULEUCC8 - 36031 - 383
13GLUGLULEULEUAA8 - 36031 - 383
23GLUGLULEULEUDD8 - 36031 - 383
14SERSERPROPROAA7 - 36130 - 384
24SERSERPROPROEE7 - 36130 - 384
15GLUGLULEULEUAA8 - 36031 - 383
25GLUGLULEULEUFF8 - 36031 - 383
16GLUGLULEULEUAA8 - 36031 - 383
26GLUGLULEULEUGG8 - 36031 - 383
17GLUGLULEULEUAA8 - 36031 - 383
27GLUGLULEULEUHH8 - 36031 - 383
18GLUGLUTHRTHRBB8 - 36231 - 385
28GLUGLUTHRTHRCC8 - 36231 - 385
19GLUGLUTHRTHRBB8 - 36231 - 385
29GLUGLUTHRTHRDD8 - 36231 - 385
110SERSERPROPROBB7 - 36130 - 384
210SERSERPROPROEE7 - 36130 - 384
111GLUGLUPROPROBB8 - 36131 - 384
211GLUGLUPROPROFF8 - 36131 - 384
112GLUGLUPROPROBB8 - 36131 - 384
212GLUGLUPROPROGG8 - 36131 - 384
113GLUGLUPROPROBB8 - 36131 - 384
213GLUGLUPROPROHH8 - 36131 - 384
114GLUGLUTHRTHRCC8 - 36231 - 385
214GLUGLUTHRTHRDD8 - 36231 - 385
115GLUGLUPROPROCC8 - 36131 - 384
215GLUGLUPROPROEE8 - 36131 - 384
116GLUGLULEULEUCC8 - 36031 - 383
216GLUGLULEULEUFF8 - 36031 - 383
117GLUGLULEULEUCC8 - 36031 - 383
217GLUGLULEULEUGG8 - 36031 - 383
118GLUGLULEULEUCC8 - 36031 - 383
218GLUGLULEULEUHH8 - 36031 - 383
119GLUGLUPROPRODD8 - 36131 - 384
219GLUGLUPROPROEE8 - 36131 - 384
120GLUGLULEULEUDD8 - 36031 - 383
220GLUGLULEULEUFF8 - 36031 - 383
121GLUGLULEULEUDD8 - 36031 - 383
221GLUGLULEULEUGG8 - 36031 - 383
122GLUGLULEULEUDD8 - 36031 - 383
222GLUGLULEULEUHH8 - 36031 - 383
123GLUGLUPROPROEE8 - 36131 - 384
223GLUGLUPROPROFF8 - 36131 - 384
124GLUGLUPROPROEE8 - 36131 - 384
224GLUGLUPROPROGG8 - 36131 - 384
125GLUGLUPROPROEE8 - 36131 - 384
225GLUGLUPROPROHH8 - 36131 - 384
126GLUGLUPROPROFF8 - 36131 - 384
226GLUGLUPROPROGG8 - 36131 - 384
127GLUGLUPROPROFF8 - 36131 - 384
227GLUGLUPROPROHH8 - 36131 - 384
128GLUGLUPROPROGG8 - 36131 - 384
228GLUGLUPROPROHH8 - 36131 - 384

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

#1: Protein
Uncharacterized protein / L-Asparaginase 1


Mass: 41977.418 Da / Num. of mol.: 8 / Fragment: catalytic domain (UNP residues 1-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: ASPG / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) C41 / References: UniProt: H0W0T5, asparaginase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE CRYSTALLIZATION EXPERIMENTS WERE SET UP WITH N-TERMINAL HIS-TAGGED FULL ...AUTHORS STATE THAT THE CRYSTALLIZATION EXPERIMENTS WERE SET UP WITH N-TERMINAL HIS-TAGGED FULL LENGTH (1-565) PROTEIN. HOWEVER, UPON SOLVING THE STRUCTURE IT BECAME CLEAR THAT THE C-TERMINAL DOMAIN HAD BEEN CLEAVED OFF IN THE DROP, LEAVING ONLY THE ASPARAGINASE CATALYTIC DOMAIN. SINCE THE EXACT LOCATION OF THE CLEAVAGE SITE IS UNKNOWN, THE SEQRES RECORDS IN THE PDB FILE ONLY INCLUDE THE 23-RESIDUE HIS TAG AND UNIPROT SEQUENCE DATABASE RESIDUES 1 THROUGH 362.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 15% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→120.46 Å / Num. obs: 146207 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.34 Å / % possible all: 98.5

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.8.0069refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HIM

2him


Resolution: 2.2→29.617 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.835 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 7281 5 %RANDOM
Rwork0.20694 ---
obs0.20849 138245 99.18 %-
all-145526 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.191 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.18 Å2
2--0.41 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21650 0 120 892 22662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922250
X-RAY DIFFRACTIONr_bond_other_d0.0060.0222029
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.99230244
X-RAY DIFFRACTIONr_angle_other_deg1.065350699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82352823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90223.725859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.983153772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.81715144
X-RAY DIFFRACTIONr_chiral_restr0.0720.23546
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02124676
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024762
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_it2.7793.53211304
X-RAY DIFFRACTIONr_mcbond_other2.7783.53211303
X-RAY DIFFRACTIONr_mcangle_it4.5715.28914114
X-RAY DIFFRACTIONr_mcangle_other4.8925.24114096
X-RAY DIFFRACTIONr_scbond_it3.0293.90810946
X-RAY DIFFRACTIONr_scbond_other3.5743.93410947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8365.73916143
X-RAY DIFFRACTIONr_long_range_B_refined7.9435.72917659
X-RAY DIFFRACTIONr_long_range_B_other7.93635.79817404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A220400.05
12B220400.05
21A225160.05
22C225160.05
31A224580.05
32D224580.05
41A222850.05
42E222850.05
51A225800.04
52F225800.04
61A225440.04
62G225440.04
71A225810.04
72H225810.04
81B220510.05
82C220510.05
91B222040.04
92D222040.04
101B221170.05
102E221170.05
111B221770.04
112F221770.04
121B221800.04
122G221800.04
131B220560.05
132H220560.05
141C225490.05
142D225490.05
151C222260.06
152E222260.06
161C226070.05
162F226070.05
171C225640.05
172G225640.05
181C225880.05
182H225880.05
191D223460.05
192E223460.05
201D225590.04
202F225590.04
211D226520.04
212G226520.04
221D224740.05
222H224740.05
231E223570.05
232F223570.05
241E223180.05
242G223180.05
251E222460.05
252H222460.05
261F227560.03
262G227560.03
271F227220.04
272H227220.04
281G226890.04
282H226890.04
LS refinement shellResolution: 2.2→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 504 -
Rwork0.341 9854 -
obs--95.98 %

+
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