[English] 日本語
Yorodumi
- PDB-4q04: Crystal structure of URE3-BP from Entomaeba histolytica without c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q04
TitleCrystal structure of URE3-BP from Entomaeba histolytica without calcium
ComponentsURE3-BP sequence specific DNA binding protein
KeywordsDNA BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / sequence specific / calcium dependent inhibition / transcription factor / TRANSCRIPTION
Function / homology
Function and homology information


COPII vesicle coating / calcium-dependent protein binding / calcium ion binding
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URE3-BP sequence specific DNA binding protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of URE3-BP from Entomaeba histolytica
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: URE3-BP sequence specific DNA binding protein
B: URE3-BP sequence specific DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7937
Polymers51,5342
Non-polymers2585
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-60 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.420, 69.420, 187.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-416-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein URE3-BP sequence specific DNA binding protein


Mass: 25767.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: URE3-BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GSV7

-
Non-polymers , 5 types, 290 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: EnhiA.01648.a.D11.PD00049 at 11.96 mg/mL against Precipitant Synergy block 2, 20.1% PEG 1500, 2.01% MPD, 0.2 M magnesium sulfate, 0.1 M sodium acetate pH 5.5, crystal tracking ID 248792c5, ...Details: EnhiA.01648.a.D11.PD00049 at 11.96 mg/mL against Precipitant Synergy block 2, 20.1% PEG 1500, 2.01% MPD, 0.2 M magnesium sulfate, 0.1 M sodium acetate pH 5.5, crystal tracking ID 248792c5, unique puck ID cjw8-9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 21, 2013 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 37199 / Num. obs: 33977 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 25.002 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.014 / Net I/σ(I): 20.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.2393.184746239089.6
1.95-20.2084.286567247693.5
2-2.060.1786.118343241194.4
2.06-2.120.1618.4411119236295.1
2.12-2.190.14911.1214361226494.7
2.19-2.270.12314.2215198221294.4
2.27-2.360.11515.6114675212494
2.36-2.450.117.8314145203493.2
2.45-2.560.08920.0413606195292.9
2.56-2.690.07822.3212859185092.3
2.69-2.830.07324.5912210174091.3
2.83-30.06626.0311784166690.8
3-3.210.05729.9510858154090
3.21-3.470.0534.910168144889
3.47-3.80.04240.599061131188.3
3.8-4.250.03844.848154117886.7
4.25-4.910.03347.757418104585.7
4.91-6.010.0343.52644787783.8
6.01-8.50.02841.92520069481.9
8.50.02151.14276040375.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.88 Å
Translation3.5 Å19.88 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SJS

3sjs


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8674 / SU B: 7.247 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1702 / SU Rfree: 0.1633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1720 5.1 %RANDOM
Rwork0.182 ---
obs0.1849 33961 91.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.19 Å2 / Biso mean: 19.677 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 14 285 3748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023603
X-RAY DIFFRACTIONr_bond_other_d0.0020.023327
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9494897
X-RAY DIFFRACTIONr_angle_other_deg0.86937623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02223.254169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89815584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2511521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_mcbond_it1.0751.3911714
X-RAY DIFFRACTIONr_mcbond_other1.0751.391713
X-RAY DIFFRACTIONr_mcangle_it1.682.082142
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 112 -
Rwork0.246 2275 -
all-2387 -
obs--89.6 %
Refinement TLS params.

S21: -0.0126 Å ° / 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 °)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)
10.3997-0.12680.0330.78780.16410.5334-0.05370.01740.01050.0844-0.05460.03190.0423-0.03070.0172-0.00410.01070.0169-0.00380.033717.14713.871165.5373
20.50260.0539-0.02850.5426-0.0760.1722-0.02920.06090.03390.01340.01370.0204-0.05690.01580.0058-0.00780.00420.0413-0.0050.0163-14.44611.423676.074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 220
2X-RAY DIFFRACTION2B7 - 220

+
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://pdbjlvh1.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