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- PDB-6qv5: Crystal structure of the CHAD domain from the plant Ricinus communis -

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Basic information

Entry
Database: PDB / ID: 6qv5
TitleCrystal structure of the CHAD domain from the plant Ricinus communis
ComponentsCHAD domain
KeywordsNUCLEAR PROTEIN / four-helix bundle / inorganic polyphosphate binding protein / all alpha-helical protein
Function / homologyCHAD domain superfamily / CHAD domain / CHAD / CHAD domain / CHAD domain profile. / CHAD domain-containing protein
Function and homology information
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLorenzo-Orts, L. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council310856 Switzerland
CitationJournal: Life Sci Alliance / Year: 2019
Title: Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules.
Authors: Lorenzo-Orts, L. / Hohmann, U. / Zhu, J. / Hothorn, M.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3423
Polymers33,2141
Non-polymers1272
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-24 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.427, 116.427, 119.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CHAD domain


Mass: 33214.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Tissue: leaves / Gene: RCOM_0386350 / Plasmid: pMH-HT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B9T8Q5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 3 M NaCl, 0.1 M Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999859 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999859 Å / Relative weight: 1
ReflectionResolution: 2.3→41.65 Å / Num. obs: 40129 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 59.44 Å2 / CC1/2: 1 / Rrim(I) all: 0.172 / Rsym value: 0.168 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 21.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6493 / CC1/2: 0.5 / Rrim(I) all: 3.677 / Rsym value: 3.591 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.65 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1083 4.98 %RANDOM
Rwork0.232 ---
obs0.232 21737 100 %-
Displacement parametersBiso mean: 83.79 Å2
Baniso -1Baniso -2Baniso -3
1-3.7553 Å20 Å20 Å2
2--3.7553 Å20 Å2
3----7.5105 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 2.3→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 5 27 2255
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082281HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893089HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d810SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes397HARMONIC5
X-RAY DIFFRACTIONt_it2281HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.67
X-RAY DIFFRACTIONt_other_torsion18.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2587SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2254 -3.68 %
Rwork0.2844 419 -
all0.2819 435 -
obs--97.76 %
Refinement TLS params.Method: refined / Origin x: 76.3871 Å / Origin y: 13.4491 Å / Origin z: 15.0526 Å
111213212223313233
T-0.2944 Å20.0172 Å20.0897 Å2--0.3291 Å20.1087 Å2--0.3498 Å2
L4.217 °2-0.0464 °20.0874 °2-3.7408 °2-0.9209 °2--1.2846 °2
S-0.0038 Å °0.0329 Å °0.4735 Å °-0.2836 Å °-0.1269 Å °-0.3885 Å °0.0594 Å °0.1331 Å °0.1308 Å °
Refinement TLS groupSelection details: { A|* }

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