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- PDB-6cdb: Crystal Structure of V66L CzrA in the Zn(II)bound state -

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Basic information

Entry
Database: PDB / ID: 6cdb
TitleCrystal Structure of V66L CzrA in the Zn(II)bound state
ComponentsArsR family transcriptional regulator
KeywordsTRANSCRIPTION / transcription regulator / Zn-binding protein / DNA binding protein / ArsR
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 ...: / 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 / Resolution: 1.99 Å
AuthorsCapdevila, D.A. / Campanello, G. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118157 United States
Pew Charitable Trusts United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System.
Authors: Capdevila, D.A. / Edmonds, K.A. / Campanello, G.C. / Wu, H. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
History
DepositionFeb 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ArsR family transcriptional regulator
B: ArsR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,53310
Polymers24,0432
Non-polymers4908
Water1,40578
1
A: ArsR family transcriptional regulator
hetero molecules

A: ArsR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,82114
Polymers24,0432
Non-polymers77812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area4090 Å2
ΔGint-144 kcal/mol
Surface area9970 Å2
MethodPISA
2
B: ArsR family transcriptional regulator
hetero molecules

B: ArsR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2456
Polymers24,0432
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area4300 Å2
ΔGint-110 kcal/mol
Surface area10230 Å2
MethodPISA
3
A: ArsR family transcriptional regulator
hetero molecules

A: ArsR family transcriptional regulator
hetero molecules

B: ArsR family transcriptional regulator
hetero molecules

B: ArsR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,06720
Polymers48,0874
Non-polymers98016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_576-x,-y+2,z+11
Buried area10290 Å2
ΔGint-292 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.546, 73.360, 50.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ArsR family transcriptional regulator / CzrA protein / HTH-type transcriptional repressor CzrA / Putative HTH-type transcriptional ...CzrA protein / HTH-type transcriptional repressor CzrA / Putative HTH-type transcriptional repressor CzrA / Repressor protein / Transcriptional regulator / Zn(II) or Co(II)-specific transcriptional repressor protein


Mass: 12021.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: rzcA, CzrA, czrA, AFO97_05125, B9Z04_11610, B9Z08_13310, BJI53_13345, BN1321_350009, EP54_06885, EQ90_13065, ERS072738_01903, ERS072840_01825, HMPREF3211_00009
Production host: Escherichia coli (E. coli) / References: UniProt: O85142

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Non-polymers , 5 types, 86 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Ches (pH 9.5), 200 mM NaCl and 10% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→41.41 Å / Num. obs: 13796 / % possible obs: 96.1 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.073 / Rsym value: 0.067 / Net I/σ(I): 19.3
Reflection shellResolution: 1.99→2.14 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.806 / Rpim(I) all: 0.313 / Rrim(I) all: 0.782 / Rsym value: 0.716 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.99→29.608 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.2275 677 4.91 %
Rwork0.1954 --
obs0.197 13775 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.09 Å2 / Biso mean: 38.3334 Å2 / Biso min: 23.07 Å2
Refinement stepCycle: final / Resolution: 1.99→29.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 20 78 1623
Biso mean--43.95 42.88 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071563
X-RAY DIFFRACTIONf_angle_d0.8222093
X-RAY DIFFRACTIONf_chiral_restr0.046248
X-RAY DIFFRACTIONf_plane_restr0.004261
X-RAY DIFFRACTIONf_dihedral_angle_d13.87961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.14360.311130.255926822795100
2.1436-2.35920.24141240.22232255237984
2.3592-2.70040.24741360.211327002836100
2.7004-3.40150.23791660.211127052871100
3.4015-29.6110.20031380.16722756289496

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