[English] 日本語
Yorodumi
- PDB-4ojh: The crystal structure of truncated, Y86E mutant of S. solfataricu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ojh
TitleThe crystal structure of truncated, Y86E mutant of S. solfataricus acylphosphatase
ComponentsAcylphosphatase
KeywordsHYDROLASE / native-like aggregation / amyloid aggregation / acylphosphatase
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Authorsde Rosa, M. / Bolognesi, M. / Ricagno, S.
CitationJournal: Febs J. / Year: 2014
Title: Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase.
Authors: de Rosa, M. / Bemporad, F. / Pellegrino, S. / Chiti, F. / Bolognesi, M. / Ricagno, S.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Oct 1, 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_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_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: Acylphosphatase
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9099
Polymers23,2362
Non-polymers6727
Water2,216123
1
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9064
Polymers11,6181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0025
Polymers11,6181
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.680, 45.190, 44.120
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Acylphosphatase / / Acylphosphate phosphohydrolase


Mass: 11618.239 Da / Num. of mol.: 2 / Mutation: Y86E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: acyP, SSO0887 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZL0, acylphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.79 Å3/Da / Density % sol: 31.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2M ammonium sulfate, 30% PEG 8000, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2013
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→31.54 Å / Num. obs: 21048 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 12.864 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 6340 / % possible all: 80.5

-
Processing

Software
NameVersionClassification
MXcube2data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OJ3

4oj3


Resolution: 1.6→31.54 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1999 9.5 %lattice symmetry 10%
Rwork0.1911 ---
obs0.1956 21033 96.54 %-
all-21786 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 35 123 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121479
X-RAY DIFFRACTIONf_angle_d1.3991991
X-RAY DIFFRACTIONf_dihedral_angle_d13.03545
X-RAY DIFFRACTIONf_chiral_restr0.098204
X-RAY DIFFRACTIONf_plane_restr0.007254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28231110.21051035X-RAY DIFFRACTION74
1.64-1.68440.25691180.19861194X-RAY DIFFRACTION85
1.6844-1.73390.24851360.19821327X-RAY DIFFRACTION94
1.7339-1.78990.22461490.19191366X-RAY DIFFRACTION99
1.7899-1.85380.2361440.18731397X-RAY DIFFRACTION100
1.8538-1.92810.21821520.1751400X-RAY DIFFRACTION100
1.9281-2.01580.27411530.18191398X-RAY DIFFRACTION100
2.0158-2.1220.20831440.18621403X-RAY DIFFRACTION100
2.122-2.2550.24821510.18071405X-RAY DIFFRACTION100
2.255-2.4290.25381500.17861394X-RAY DIFFRACTION100
2.429-2.67330.23691450.20251411X-RAY DIFFRACTION100
2.6733-3.05990.25911460.19691421X-RAY DIFFRACTION100
3.0599-3.85410.24151530.19551423X-RAY DIFFRACTION100
3.8541-31.54990.20511470.19381460X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6003-3.01964.38796.7141-5.04086.98180.20570.3125-0.0206-0.6517-0.0121-0.15250.25120.0433-0.16490.13960.01110.04130.15260.00020.085622.0202-6.52687.2762
21.2229-0.39450.54735.9793-0.86671.20940.01490.00360.0131-0.2352-0.0027-0.0010.006-0.0066-0.01010.0431-0.00260.02180.069-0.00570.079618.2236-5.234216.9216
34.907-0.73821.37964.3393-1.54485.38790.00140.32160.3604-0.303-0.0963-0.1702-0.24270.30370.08990.11890.0070.03920.09940.01080.093122.41760.13779.1926
41.8044-0.37352.36770.4066-0.77863.36560.21950.3818-0.0147-0.3538-0.2045-0.12230.0610.09320.04480.17180.03840.01320.1690.0150.086727.9302-7.150912.7861
52.6824-0.99081.6352.8639-2.90863.68220.0410.0695-0.2528-0.46990.05740.32640.2957-0.7021-0.07370.17770.0072-0.04240.1859-0.03660.206310.2977-3.89788.1434
64.26833-3.95025.964-3.78274.88870.0807-0.2125-0.03790.49380.0625-0.0481-0.1034-0.1998-0.10530.1248-0.0047-0.01160.15210.0240.07211.0386-1.370836.4787
71.31390.9666-0.56285.8868-1.16391.0796-0.0113-0.0442-0.08450.12950.05690.0850.0336-0.0974-0.04560.0384-0.0016-0.00420.09020.00230.0944-2.5894-3.242727.1396
84.65931.2963-1.44086.1916-1.49145.9197-0.0247-0.2676-0.49810.25780.0378-0.09690.44260.2186-0.00050.1068-0.0088-0.03820.11040.01470.1241.5437-8.553634.8909
93.02770.2839-2.92412.28920.51016.10480.0633-0.32650.0170.2154-0.1354-0.14730.09650.23330.0570.07610.0004-0.00890.10640.01990.09976.9154-1.141931.3093
103.50430.4755-0.86172.9763-0.6033.0251-0.0274-0.4672-0.14060.51290.09950.542-0.0203-0.8427-0.04090.16520.00070.0740.29620.02520.2496-10.8468-4.791436.0354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 89 )
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 101 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 23 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 101 )

+
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