[English] 日本語
Yorodumi
- PDB-5c9b: Crystal structure of a retropepsin-like aspartic protease from Ri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c9b
TitleCrystal structure of a retropepsin-like aspartic protease from Rickettsia conorii
ComponentsApRick protease
KeywordsHYDROLASE / pepsin / ApRick
Function / homology
Function and homology information


acyltransferase activity / aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Clan AA aspartic peptidase, C-terminal / Retropepsin-like domain, bacterial / gag-polyprotein putative aspartyl protease / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesRickettsia conorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLi, M. / Gustchina, A. / Cruz, R. / Simoes, M. / Curto, P. / Martinez, J. / Faro, C. / Simoes, I. / Wlodawer, A.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease.
Authors: Li, M. / Gustchina, A. / Cruz, R. / Simoes, M. / Curto, P. / Martinez, J. / Faro, C. / Simoes, I. / Wlodawer, A.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ApRick protease
B: ApRick protease
C: ApRick protease
D: ApRick protease


Theoretical massNumber of molelcules
Total (without water)63,4514
Polymers63,4514
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.985, 101.985, 127.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-303-

HOH

21C-324-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B94 - 224
2114A94 - 224
1124C94 - 224
2124A94 - 224
1134D94 - 224
2134A94 - 224
1144B94 - 224
2144C94 - 224
1154B94 - 224
2154D94 - 224
1164C94 - 224
2164D94 - 224

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.920767, -0.311318, -0.235092), (-0.227118, -0.06218, 0.97188), (-0.317182, 0.948269, -0.013453)113.02625, -42.62558, 74.21591

-
Components

#1: Protein
ApRick protease


Mass: 15862.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia conorii (bacteria) / Gene: RC1339 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92FY8, Hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 24% PEG4000, 0.2 M lithium sulfate, pH 5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9825 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9825 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 31615 / Num. obs: 28761 / % possible obs: 87.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 31.27
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.67 / % possible all: 33.6

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementResolution: 2.4→47.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.365 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26222 1458 5.1 %RANDOM
Rwork0.19893 ---
obs0.20206 27301 91.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.462 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å21.1 Å2-0 Å2
2--1.1 Å2-0 Å2
3----3.56 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 0 128 4020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193948
X-RAY DIFFRACTIONr_bond_other_d0.0020.023987
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9775295
X-RAY DIFFRACTIONr_angle_other_deg0.83939142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2424.286168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51115718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5631519
X-RAY DIFFRACTIONr_chiral_restr0.1060.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02890
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_it10.5338.751958
X-RAY DIFFRACTIONr_mcbond_other10.5018.751957
X-RAY DIFFRACTIONr_mcangle_it13.06316.2812430
X-RAY DIFFRACTIONr_mcangle_other13.0716.2842431
X-RAY DIFFRACTIONr_scbond_it14.99610.8261990
X-RAY DIFFRACTIONr_scbond_other14.99210.8261991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.54418.9542866
X-RAY DIFFRACTIONr_long_range_B_refined20.64337.2064271
X-RAY DIFFRACTIONr_long_range_B_other20.68237.1744256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2017MEDIUM POSITIONAL0.790.5
1B2017MEDIUM THERMAL9.442
2C1969MEDIUM POSITIONAL0.780.5
2C1969MEDIUM THERMAL12.922
3D1838MEDIUM POSITIONAL0.430.5
3D1838MEDIUM THERMAL16.752
4B1988MEDIUM POSITIONAL0.520.5
4B1988MEDIUM THERMAL122
5B1838MEDIUM POSITIONAL0.630.5
5B1838MEDIUM THERMAL18.372
6C1838MEDIUM POSITIONAL0.660.5
6C1838MEDIUM THERMAL11.992
LS refinement shellResolution: 2.37→2.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 55 -
Rwork0.349 961 -
obs--44.02 %
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)
10.154-0.03040.16530.0167-0.09850.8026-0.0550.0659-0.04250.0093-0.0344-0.0114-0.0333-0.05450.08940.4129-0.1359-0.05870.26870.00080.073448.786814.387139.2249
20.0765-0.11640.05090.24620.07740.7088-0.0027-0.0707-0.0216-0.02580.1220.0630.02260.1522-0.11930.3439-0.1322-0.03740.27650.00390.131854.3949-16.515372.0166
31.29450.81220.47220.60060.17680.33760.2106-0.1197-0.21870.099-0.1346-0.12660.12690.0159-0.0760.4525-0.117-0.0560.22570.02640.090170.06210.812472.1183
40.57630.22480.0730.1769-0.11170.23070.114-0.06850.01650.20840.03970.0994-0.2403-0.1026-0.15370.3690.07260.11290.26310.04380.208428.42549.022959.8988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A104 - 234
2X-RAY DIFFRACTION2B104 - 234
3X-RAY DIFFRACTION3C104 - 234
4X-RAY DIFFRACTION4D104 - 234

+
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