[English] 日本語
Yorodumi
- PDB-4r5c: Crystal structure of computational designed leucine rich repeats ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r5c
TitleCrystal structure of computational designed leucine rich repeats DLRR_E in space group of P212121
ComponentsLeucine rich repeat protein
KeywordsDE NOVO PROTEIN / Leucine rich repeat (LRR) protein
Function / homologyLeucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsShen, B.W. / Stoddard, B.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Control of repeat-protein curvature by computational protein design.
Authors: Park, K. / Shen, B.W. / Parmeggiani, F. / Huang, P.S. / Stoddard, B.L. / Baker, D.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 18, 2015Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3633
Polymers33,2391
Non-polymers1242
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.137, 77.707, 101.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Leucine rich repeat protein


Mass: 33239.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG 1000 v/v, 0.1 M Na/K phosphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2014
RadiationMonochromator: single crystal Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.93→42.6 Å / Num. all: 20114 / Num. obs: 19993 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rsym value: 0.063 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.93-2500.171196
2-2.085.810.30.144198.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→42.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.216 / SU ML: 0.102 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22216 1011 5.1 %RANDOM
Rwork0.15688 ---
obs0.16017 18923 99.83 %-
all-19993 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.949 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---2.43 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.93→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 8 112 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192396
X-RAY DIFFRACTIONr_bond_other_d0.0010.022354
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9753269
X-RAY DIFFRACTIONr_angle_other_deg0.88235401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.30827.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3915429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.228156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
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_it1.1951.2721230
X-RAY DIFFRACTIONr_mcbond_other1.1941.2691229
X-RAY DIFFRACTIONr_mcangle_it1.8181.8951541
X-RAY DIFFRACTIONr_mcangle_other1.8081.9561543
X-RAY DIFFRACTIONr_scbond_it2.2441.631166
X-RAY DIFFRACTIONr_scbond_other2.2331.661184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4832.3691752
X-RAY DIFFRACTIONr_long_range_B_refined6.60611.2532718
X-RAY DIFFRACTIONr_long_range_B_other6.59711.1752709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 83 -
Rwork0.171 1373 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: 25.7703 Å / Origin y: 10.4839 Å / Origin z: -13.8362 Å
111213212223313233
T0.0103 Å2-0.0139 Å20.0059 Å2-0.154 Å2-0.0025 Å2--0.0804 Å2
L0.6058 °2-0.7683 °2-0.2082 °2-4.6424 °20.2898 °2--1.0412 °2
S0.0336 Å °0.0468 Å °-0.004 Å °-0.0907 Å °-0.0421 Å °0.1101 Å °-0.0758 Å °-0.0768 Å °0.0085 Å °

+
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