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- PDB-1r22: Crystal structure of the cyanobacterial metallothionein repressor... -

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Basic information

Entry
Database: PDB / ID: 1r22
TitleCrystal structure of the cyanobacterial metallothionein repressor SmtB (C14S/C61S/C121S mutant) in the Zn2alpha5-form
ComponentsTranscriptional repressor smtB
KeywordsTRANSCRIPTION REPRESSOR / Zinc / DNA binding protein / transcriptional regulation / winged HTH protein
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / 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 ...ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / 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 repressor SmtB
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional repressor smtB
B: Transcriptional repressor smtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1574
Polymers27,0272
Non-polymers1312
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-107 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.448, 124.678, 25.909
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 as contained in the asymmetric unit.

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Components

#1: Protein Transcriptional repressor smtB


Mass: 13513.278 Da / Num. of mol.: 2 / Mutation: C14S, C61S, C121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Species: Synechococcus elongatus / Strain: PCC7942 / Gene: SMTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30340
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na/K phosphate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.2398, 1.2828, 1.2833
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.23981
21.28281
31.28331
ReflectionResolution: 2.3→50 Å / Num. all: 9876 / Num. obs: 9318 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.069 / Net I/σ(I): 12.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rsym value: 0.271 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.878 / SU B: 7.618 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28962 442 4.8 %RANDOM
Rwork0.22878 ---
all0.23015 9834 --
obs0.23015 8841 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.456 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2--0.76 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 2 60 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211530
X-RAY DIFFRACTIONr_bond_other_d0.0360.021435
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.9562073
X-RAY DIFFRACTIONr_angle_other_deg1.95633296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1440.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021721
X-RAY DIFFRACTIONr_gen_planes_other0.0270.02319
X-RAY DIFFRACTIONr_nbd_refined0.2350.2387
X-RAY DIFFRACTIONr_nbd_other0.2460.21733
X-RAY DIFFRACTIONr_nbtor_other0.0970.21000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4571.5949
X-RAY DIFFRACTIONr_mcangle_it2.59621505
X-RAY DIFFRACTIONr_scbond_it3.4923581
X-RAY DIFFRACTIONr_scangle_it5.7224.5568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.305→2.364 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 26
Rwork0.229 577

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