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- PDB-1r1v: Crystal structure of the metal-sensing transcriptional repressor ... -

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Basic information

Entry
Database: PDB / ID: 1r1v
TitleCrystal structure of the metal-sensing transcriptional repressor CzrA from Staphylococcus aureus in the Zn2-form
Componentsrepressor protein
KeywordsTRANSCRIPTION REPRESSOR / DNA binding / transcriptional regulation / winged HTH protein
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEicken, C. / Pennella, M.A. / Chen, X. / Koshlap, K.M. / VanZile, M.L. / Sacchettini, J.C. / Giedroc, D.P.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A metal-ligand-mediated intersubunit allosteric switch in related SmtB/ArsR zinc sensor proteins.
Authors: Eicken, C. / Pennella, M.A. / Chen, X. / Koshlap, K.M. / VanZile, M.L. / Sacchettini, J.C. / Giedroc, D.P.
History
DepositionSep 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: repressor protein
B: repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2776
Polymers24,0152
Non-polymers2624
Water3,999222
1
A: repressor protein
hetero molecules

A: repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,53910
Polymers24,0152
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area3290 Å2
ΔGint-109 kcal/mol
Surface area10000 Å2
MethodPISA, PQS
2
B: repressor protein

B: repressor protein


Theoretical massNumber of molelcules
Total (without water)24,0152
Polymers24,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area3370 Å2
ΔGint-106 kcal/mol
Surface area10200 Å2
MethodPISA, PQS
3
A: repressor protein
B: repressor protein
hetero molecules

A: repressor protein
B: repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,55412
Polymers48,0314
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area8560 Å2
ΔGint-294 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.444, 75.370, 50.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a homodimer generated from the two monomers in the asymmetric unit by the operations:

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Components

#1: Protein repressor protein / CzrA


Mass: 12007.708 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: czrA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O85142
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 8000, NaCl, Ches, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→60 Å / Num. all: 9754 / Num. obs: 9503 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 5.7 % / Rsym value: 0.049 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.122 / % possible all: 91.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R1T

1r1t


Resolution: 2.3→60 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 949 -RANDOM
Rwork0.195 ---
all0.208 9492 --
obs0.205 9215 94.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.633 Å20 Å20 Å2
2---10.851 Å20 Å2
3----3.781 Å2
Refinement stepCycle: LAST / Resolution: 2.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 4 222 1742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.017
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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