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- PDB-1q0a: Crystal structure of the Zn(II) form of E. coli ZntR, a zinc-sens... -

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Basic information

Entry
Database: PDB / ID: 1q0a
TitleCrystal structure of the Zn(II) form of E. coli ZntR, a zinc-sensing transcriptional regulator (space group C222)
ComponentsZn(II)-responsive regulator of zntA
KeywordsTRANSCRIPTION / MerR family transcriptional regulator / Zn(II)-responsive regulator of zntA
Function / homology
Function and homology information


DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
Zn(II)-responsive transcriptional regulator / MerR, DNA binding / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain ...Zn(II)-responsive transcriptional regulator / MerR, DNA binding / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator ZntR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChangela, A. / Chen, K. / Xue, Y. / Holschen, J. / Outten, C.E. / O'Halloran, T.V. / Mondragon, A.
CitationJournal: Science / Year: 2003
Title: Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR
Authors: Changela, A. / Chen, K. / Xue, Y. / Holschen, J. / Outten, C.E. / O'Halloran, T.V. / Mondragon, A.
History
DepositionJul 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / 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_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_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_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.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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zn(II)-responsive regulator of zntA
B: Zn(II)-responsive regulator of zntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7429
Polymers22,2232
Non-polymers5197
Water2,342130
1
B: Zn(II)-responsive regulator of zntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3384
Polymers11,1121
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-185 kcal/mol
Surface area14720 Å2
MethodPISA
3
A: Zn(II)-responsive regulator of zntA
hetero molecules

A: Zn(II)-responsive regulator of zntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,80810
Polymers22,2232
Non-polymers5858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5770 Å2
ΔGint-277 kcal/mol
Surface area10700 Å2
MethodPISA, PQS
4
B: Zn(II)-responsive regulator of zntA
hetero molecules

B: Zn(II)-responsive regulator of zntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6778
Polymers22,2232
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)84.666, 170.707, 42.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
DetailsFor chain A, apply the following symmetry operations to generate the biologically significant dimer: -x, y, -z / For chain B, apply the following symmetry operations to generate the biologically significant dimer: 1-x, y, 2-z

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Components

#1: Protein Zn(II)-responsive regulator of zntA


Mass: 11111.611 Da / Num. of mol.: 2 / Fragment: Dimerization and metal-binding domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ZNTR / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ACS5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na/K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.52 Msodium potassium phosphate1reservoir
20.08 %(v/v)saturatedHEPES1reservoirpH7.5
34 mg/mlprotein1drop
45 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→24 Å / Num. obs: 21722 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.039 / Net I/σ(I): 13
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1339 / Rsym value: 0.156 / % possible all: 83

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ZntR in P212121 crystal form

Resolution: 2→23.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1440953.75 / Data cutoff high rms absF: 1440953.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: partially refined structure
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1034 4.9 %RANDOM
Rwork0.229 ---
obs0.229 21195 100 %-
all-21722 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9013 Å2 / ksol: 0.38242 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2---1.99 Å20 Å2
3---4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→23.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 15 130 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 160 4.6 %
Rwork0.24 3324 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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