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- PDB-2hh7: Crystal Structure of Cu(I) bound CsoR from Mycobacterium tuberculosis. -

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Basic information

Entry
Database: PDB / ID: 2hh7
TitleCrystal Structure of Cu(I) bound CsoR from Mycobacterium tuberculosis.
ComponentsHypothetical protein CsoR
KeywordsUNKNOWN FUNCTION / 4-helix bundle
Function / homology
Function and homology information


copper ion sensor activity / response to silver ion / response to copper ion / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / copper ion binding / negative regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm
Similarity search - Function
Metal-sensitive repressor, helix protomer / Metal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (I) ION / Copper-sensing transcriptional repressor CsoR / Copper-sensing transcriptional repressor CsoR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsSacchettini, J.C. / Ramesh, A.
CitationJournal: Nat.Chem.Biol. / Year: 2007
Title: CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator.
Authors: Liu, T. / Ramesh, A. / Ma, Z. / Ward, S.K. / Zhang, L. / George, G.N. / Talaat, A.M. / Sacchettini, J.C. / Giedroc, D.P.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein CsoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8812
Polymers12,8181
Non-polymers641
Water36020
1
A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7624
Polymers25,6352
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area4130 Å2
ΔGint-60 kcal/mol
Surface area9100 Å2
MethodPISA
2
A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules

A: Hypothetical protein CsoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5258
Polymers51,2714
Non-polymers2544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area10750 Å2
ΔGint-146 kcal/mol
Surface area15710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.059, 91.059, 46.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe second part of the biological assembly is generated by the symmetry operation : x, x-y-1, -z-1/3

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Components

#1: Protein Hypothetical protein CsoR


Mass: 12817.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P71543, UniProt: P9WP49*PLUS
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% Peg4000,0.1Msodium citrate tribasic dihydrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97927
SYNCHROTRONALS 8.3.120.97962, 0.97974, 0.95373
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 27, 2005
ADSC QUANTUM 3152CCDOct 28, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979621
30.979741
40.953731
ReflectionResolution: 2.55→50 Å / Num. all: 4011 / Num. obs: 3987 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.24
Reflection shellHighest resolution: 2.55 Å / % possible all: 99.2

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Processing

Software
NameClassification
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.55→20 Å / σ(F): 4.24 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 184 random
Rwork0.231 --
all-3989 -
obs-3952 -
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 1 20 679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.267
X-RAY DIFFRACTIONf_bond_d0.011
LS refinement shellHighest resolution: 2.55 Å
RfactorNum. reflection% reflection
Rfree0.279 184 -
Rwork0.231 --
obs-3989 99.4 %

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