[English] 日本語
Yorodumi
- PDB-1u15: Crystal structure of a duck-delta-crystallin-1 double loop mutant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u15
TitleCrystal structure of a duck-delta-crystallin-1 double loop mutant (DLM)
ComponentsDelta crystallin I
KeywordsLYASE / eye lens protein / duck-delta-crystallin / argininosuccinate lyase / enzyme mechanism
Function / homology
Function and homology information


arginine biosynthetic process via ornithine / structural constituent of eye lens / catalytic activity
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTsai, M. / Sampaleanu, L.M. / Greene, C. / Creagh, L. / Haynes, C. / Howell, P.L.
CitationJournal: Biochemistry / Year: 2004
Title: A duck delta1 crystallin double loop mutant provides insight into residues important for argininosuccinate lyase activity.
Authors: Tsai, M. / Sampaleanu, L.M. / Greene, C. / Creagh, L. / Haynes, C. / Howell, P.L.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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: Delta crystallin I
B: Delta crystallin I
C: Delta crystallin I
D: Delta crystallin I


Theoretical massNumber of molelcules
Total (without water)208,8524
Polymers208,8524
Non-polymers00
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28250 Å2
ΔGint-154 kcal/mol
Surface area58960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.700, 98.800, 107.400
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Delta crystallin I


Mass: 52212.926 Da / Num. of mol.: 4
Mutation: Q22E,M23K,S25N,T26S,S29A,T30Y,E31D,L74W,I79F,T82K,Q89H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / References: UniProt: P24057, argininosuccinate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, PEG 2000 MME, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2002 / Details: Confocal multilayer
RadiationMonochromator: Confocal multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→35.19 Å / Num. obs: 66502 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 56.3 Å2 / Limit h max: 36 / Limit h min: -36 / Limit k max: 39 / Limit k min: -36 / Limit l max: 42 / Limit l min: 0 / Observed criterion F max: 943270.97 / Observed criterion F min: 9.461 / Rsym value: 0.078
Reflection shellResolution: 2.5→2.58 Å / % possible all: 98.3

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1HY1

1hy1


Resolution: 2.5→35.19 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 6627 10.1 %random
Rwork0.221 ---
obs-65379 98.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 46.3587 Å2 / ksol: 0.328746 e/Å3
Displacement parametersBiso max: 167.09 Å2 / Biso mean: 41.78 Å2 / Biso min: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å20 Å2-3.12 Å2
2---0.88 Å20 Å2
3---5.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.33 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13919 0 0 617 14536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_torsion_deg19.4
X-RAY DIFFRACTIONc_torsion_impr_deg0.88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.610.3887969.90.31372460.0148321804296.6
2.61-2.750.365808100.29372590.0138280806797.4
2.75-2.920.33683110.30.26272530.0128263808497.8
2.92-3.150.32682910.20.24372970.0118267812698.3
3.15-3.470.3147939.60.25374320.0118345822598.6
3.47-3.970.27986110.50.22373340.018283819598.9
3.97-50.21286510.50.1574040.0078349826999
5-35.190.25184410.10.20775270.0098471837198.8
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4protein.top

+
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