[English] 日本語
Yorodumi
- PDB-6cw0: Crystal structure of Cryptosporidium parvum bromodomain cgd2_2690 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cw0
TitleCrystal structure of Cryptosporidium parvum bromodomain cgd2_2690
ComponentsCgd2_2690 protein
KeywordsTRANSFERASE / bromodomain / BI2536 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-R78 / Bromo domain-containing protein / Cgd2_2690 protein
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsDong, A. / Lin, L. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of Cryptosporidium parvum bromodomain cgd2_2690
Authors: Lin, L. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Structural Genomics Consortium (SGC)
History
DepositionMar 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cgd2_2690 protein
B: Cgd2_2690 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,51015
Polymers25,1822
Non-polymers1,32813
Water5,152286
1
A: Cgd2_2690 protein
hetero molecules

B: Cgd2_2690 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,51015
Polymers25,1822
Non-polymers1,32813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1920 Å2
ΔGint-25 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.543, 71.422, 98.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cgd2_2690 protein


Mass: 12591.149 Da / Num. of mol.: 2 / Fragment: residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: cgd2_2690 / Plasmid: pET15-MHL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: F0X3M9, UniProt: A3FQ86*PLUS

-
Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N7O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5M NH4SO4 and 0.1M BTP 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 49181 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.031 / Rrim(I) all: 0.091 / Χ2: 1.421 / Net I/σ(I): 6.7 / Num. measured all: 403015
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.38-1.47.40.96924280.6990.3791.0420.589100
1.4-1.437.70.86924390.7150.330.9310.671100
1.43-1.468.20.78224000.7790.290.8350.706100
1.46-1.497.80.6224460.8640.2340.6630.763100
1.49-1.528.50.51523920.9010.1870.5490.909100
1.52-1.558.40.44624510.9170.1630.4751.013100
1.55-1.598.30.38224030.9370.140.4071.094100
1.59-1.647.90.31924380.9510.120.3411.206100
1.64-1.688.30.28424100.9580.1050.3031.168100
1.68-1.748.30.22924530.970.0840.2441.196100
1.74-1.88.10.19524510.9770.0720.2081.272100
1.8-1.878.60.16224090.9850.0580.1721.293100
1.87-1.968.50.13824480.9880.050.1471.398100
1.96-2.068.10.11124750.9930.0410.1181.666100
2.06-2.198.60.09724610.9940.0350.1031.837100
2.19-2.368.30.08624700.9950.0320.0922.02100
2.36-2.68.70.07824680.9960.0280.0832.086100
2.6-2.978.30.07225240.9960.0260.0762.223100
2.97-3.758.30.06525240.9960.0240.0692.63100
3.75-507.80.05926910.9970.0220.0632.27199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
PHASERphasing
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z93

4z93


Resolution: 1.38→50.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.981 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1515 3.2 %RANDOM
Rwork0.1762 ---
obs0.177 46541 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.66 Å2 / Biso mean: 17.809 Å2 / Biso min: 11.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.3 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.38→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 84 297 2084
Biso mean--26.29 29.74 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192007
X-RAY DIFFRACTIONr_bond_other_d0.0010.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9592751
X-RAY DIFFRACTIONr_angle_other_deg0.81834132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57426.019103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07115355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.296157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
LS refinement shellResolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 105 -
Rwork0.274 3392 -
all-3497 -
obs--100 %

+
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