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- PDB-6ahx: Copper-Sensing Operon Regulator Protein (CsoRGz) -

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Basic information

Entry
Database: PDB / ID: 6ahx
TitleCopper-Sensing Operon Regulator Protein (CsoRGz)
ComponentsPutative cytosolic protein
KeywordsMETAL BINDING PROTEIN / Copper-Sensing Operon Regulator Protein
Function / homologyMetal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / Putative cytosolic protein
Function and homology information
Biological speciesGeobacillus zalihae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNormi, M.Y. / Mangavelu, A. / Sayangku, A.A. / Jonet, M.A. / Adam, T.C.L. / Ali, M.S.M. / Rahman, R.N.Z.R.A. / Salleh, A.B.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Universiti Putra Malaysia Putra Postgraduate Initiative Grant9502200 Malaysia
CitationJournal: To Be Published
Title: Crystallization, Structural Determination and Analysis of Copper-sensing Operon Regulator Protein (CsoRGz) of Geobacillus zalihae Strain T1
Authors: Normi, M.Y. / Mangavelu, A. / Sayangku, A.A. / Jonet, M.A. / Adam, T.C.L. / Ali, M.S.M. / Rahman, R.N.Z.R.A. / Salleh, A.B.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 1, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 22, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytosolic protein


Theoretical massNumber of molelcules
Total (without water)11,7811
Polymers11,7811
Non-polymers00
Water86548
1
A: Putative cytosolic protein

A: Putative cytosolic protein


Theoretical massNumber of molelcules
Total (without water)23,5632
Polymers23,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area2750 Å2
ΔGint-28 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.730, 44.730, 82.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative cytosolic protein


Mass: 11781.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus zalihae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: S7SWX2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293.95 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5% (v/v) Tacsimate TM pH 7.0, 0.1 M HEPES pH 7.0, 10% (w/v) PEG monomethyl ether 5000
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→38.74 Å / Num. obs: 6882 / % possible obs: 100 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 45.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.028 / Num. unique obs: 664

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AAI

3aai


Resolution: 2→38.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.568 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25796 345 5.3 %RANDOM
Rwork0.1967 ---
obs0.19996 6184 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.033 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20.53 Å20 Å2
2--1.06 Å2-0 Å2
3----3.45 Å2
Refinement stepCycle: 1 / Resolution: 2→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms471 0 0 48 519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019475
X-RAY DIFFRACTIONr_bond_other_d0.0030.02495
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.971635
X-RAY DIFFRACTIONr_angle_other_deg1.03631132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.246559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00722.38121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6571596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.046156
X-RAY DIFFRACTIONr_chiral_restr0.1030.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02105
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_it2.5892.958239
X-RAY DIFFRACTIONr_mcbond_other2.5732.958238
X-RAY DIFFRACTIONr_mcangle_it3.6024.431297
X-RAY DIFFRACTIONr_mcangle_other3.64.432298
X-RAY DIFFRACTIONr_scbond_it5.2163.747236
X-RAY DIFFRACTIONr_scbond_other5.2053.747237
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3095.321339
X-RAY DIFFRACTIONr_long_range_B_refined9.79724.666580
X-RAY DIFFRACTIONr_long_range_B_other9.63824.222559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 37 -
Rwork0.28 467 -
obs--98.05 %

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