[English] 日本語
Yorodumi
- PDB-1h91: The crystal structure of lobster apocrustacyanin A1 using softer ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h91
TitleThe crystal structure of lobster apocrustacyanin A1 using softer X-rays.
ComponentsCRUSTACYANIN A1 SUBUNIT
KeywordsAPOCRUSTACYANIN / SOFTER X-RAYS / XENON / SULPHURS
Function / homology
Function and homology information


pigment binding / response to stress / extracellular region
Similarity search - Function
Invertebrate colouration protein / Lipocalin, ApoD type / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Crustacyanin-A1 subunit
Similarity search - Component
Biological speciesHOMARUS GAMMARUS (European lobster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsCianci, M. / Rizkallah, P.J. / Olczak, A. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Lobster Apocrustacyanin A1 Using Softer X-Rays
Authors: Cianci, M. / Rizkallah, P.J. / Olczak, A. / Raftery, J. / Chayen, N.E. / Zagalsky, P.F. / Helliwell, J.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Apocrustacyanin A1 from the Lobster Carotenoprotein Alpha-Crustacyanin: Crystallization and Initial X- Ray Analysis Involving Softer X-Rays
Authors: Chayen, N.E. / Cianci, M. / Olczak, A. / Raftery, J. / Rizkallah, P.J. / Zagalsky, P.F. / Helliwell, J.R.
History
DepositionFeb 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_data_processing_status / pdbx_database_proc / pdbx_database_status / pdbx_validate_close_contact / struct_biol / struct_conn / struct_conn_type
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_data_processing_status.task_name / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRUSTACYANIN A1 SUBUNIT
B: CRUSTACYANIN A1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5896
Polymers41,1162
Non-polymers4734
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.650, 80.680, 110.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.05959, 0.89915, 0.43357), (0.90361, -0.23316, 0.35934), (0.42419, 0.37036, -0.82637)
Vector: -18.24337, 22.05606, -1.03611)

-
Components

#1: Protein CRUSTACYANIN A1 SUBUNIT / APO A1


Mass: 20558.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMARUS GAMMARUS (European lobster) / Tissue: CARAPACE / References: UniProt: P58989*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID SEQUENCE IS IN GOOD AGREEMENT TO THAT DEPOSITED FOR APO CRUSTACYANIN C1 (SWS ENTRY P80029)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP, 18 DEGREES C, OVER RESERVOIR 0.1 M TRIS/HCL, PH 9.0, 5% MPD, 1MM EDTA, 1.9 M AMMONIUM SULPHATE. DROP MADE UP BY MIXING 1:1 PROTEIN SOLUTION (CONTAINING 20 MG/ML A1 SUBUNIT IN 0. ...Details: HANGING DROP, 18 DEGREES C, OVER RESERVOIR 0.1 M TRIS/HCL, PH 9.0, 5% MPD, 1MM EDTA, 1.9 M AMMONIUM SULPHATE. DROP MADE UP BY MIXING 1:1 PROTEIN SOLUTION (CONTAINING 20 MG/ML A1 SUBUNIT IN 0.1 M TRIS-HCL, PH 7.0, 1 MM EDTA) AND OF THE RESERVOIR SOLUTION.
Crystal grow
*PLUS
Temperature: 291 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
25 %MPD1reservoir
31 mMEDTA1reservoir
41.9 Mammonium sulfate1reservoir
520 mg/mlprotein1drop
60.1 MTris-HCl1drop
71 mMEDTA1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.35→100 Å / Num. obs: 73302 / % possible obs: 88.4 % / Redundancy: 8.01 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 1.35→1.42 Å / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 7.3 / % possible all: 81.8
Reflection
*PLUS
Num. measured all: 330300 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 79.4 %

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→100 Å / Num. parameters: 21239 / Num. restraintsaints: 25189 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3137 5 %RANDOM
obs0.1766 -80.1 %-
all-60276 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 30 / Occupancy sum non hydrogen: 3377.2
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 32 439 3373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0292
X-RAY DIFFRACTIONs_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1766
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.46 Å / Rfactor obs: 0.184

+
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