[English] 日本語
Yorodumi
- PDB-9d91: Crystal structure of L-asparaginase from Streptococcus pneumoniae... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d91
TitleCrystal structure of L-asparaginase from Streptococcus pneumoniae TIGR4
ComponentsAsparaginase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


asparagine metabolic process / asparaginase / asparaginase activity
Similarity search - Function
L-asparaginase, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / 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, type II / Asparaginase/glutaminase, active site 1 / Asparaginase / glutaminase active site signature 1. / 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.
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsGade, P. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of L-asparaginase from Streptococcus pneumoniae TIGR4
Authors: Gade, P. / Endres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionAug 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Asparaginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4157
Polymers34,9071
Non-polymers5086
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.369, 74.016, 132.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

21A-697-

HOH

31A-702-

HOH

-
Components

#1: Protein Asparaginase


Mass: 34907.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: ansB, A5N45_01685, AZJ70_05345, AZK02_05425, ERS019316_00818, ERS019420_01259, ERS021218_01180, GM536_02705, GM543_02955, GM545_09810, RLD18_05820, SAMEA3171064_00528, SAMEA3353485_02125, ...Gene: ansB, A5N45_01685, AZJ70_05345, AZK02_05425, ERS019316_00818, ERS019420_01259, ERS021218_01180, GM536_02705, GM543_02955, GM545_09810, RLD18_05820, SAMEA3171064_00528, SAMEA3353485_02125, SAMEA3353631_01742, SAMEA3354366_01577, SAMEA3389353_01902, SAMEA4038883_00005
Production host: Escherichia coli (E. coli) / References: UniProt: A0A062WR39, asparaginase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Lithium Sulfate, 0.1 M Tris HCl pH 7.0, 2 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 34185 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 13.21 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.042 / Rrim(I) all: 0.099 / Χ2: 0.923 / Net I/σ(I): 15.637
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 34185 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.262 / Rrim(I) all: 0.66 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→43.82 Å / SU ML: 0.158 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.6294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1883 1747 5.23 %
Rwork0.1575 31681 -
obs0.1591 33428 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.88 Å2
Refinement stepCycle: LAST / Resolution: 1.62→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 28 226 2660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592474
X-RAY DIFFRACTIONf_angle_d0.84233354
X-RAY DIFFRACTIONf_chiral_restr0.0595390
X-RAY DIFFRACTIONf_plane_restr0.0063427
X-RAY DIFFRACTIONf_dihedral_angle_d15.435902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.670.26261160.22632242X-RAY DIFFRACTION83.47
1.67-1.720.2421430.19572457X-RAY DIFFRACTION92.33
1.72-1.790.20881480.17212589X-RAY DIFFRACTION96.92
1.79-1.860.17881350.16322678X-RAY DIFFRACTION99.12
1.86-1.940.21771400.15662672X-RAY DIFFRACTION99.65
1.94-2.040.19461590.16362655X-RAY DIFFRACTION99.79
2.04-2.170.20131530.14742713X-RAY DIFFRACTION99.83
2.17-2.340.16631330.14792686X-RAY DIFFRACTION99.93
2.34-2.580.21231510.15792707X-RAY DIFFRACTION99.72
2.58-2.950.19561490.16652721X-RAY DIFFRACTION99.86
2.95-3.710.16931480.1512743X-RAY DIFFRACTION99.59
3.72-43.820.16311720.14452818X-RAY DIFFRACTION98.55
Refinement TLS params.Method: refined / Origin x: -16.1971134209 Å / Origin y: -27.9061777086 Å / Origin z: -16.5508964298 Å
111213212223313233
T0.0637113053965 Å2-0.00234091831157 Å2-0.00590902163903 Å2-0.066798753065 Å20.000341135273911 Å2--0.0612438902689 Å2
L0.303728982854 °20.0289765723672 °20.0243066856395 °2-0.252526000434 °2-0.0647336453863 °2--0.191580453728 °2
S-0.0116542367229 Å °0.0142200250086 Å °0.0220490420175 Å °0.047650615641 Å °0.00505437196703 Å °-0.0295412943281 Å °-0.0214483757702 Å °0.0192376811312 Å °-0.0502292991282 Å °
Refinement TLS groupSelection details: all

+
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