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- PDB-3f8n: Crystal structure of PerR-Zn-Mn -

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Basic information

Entry
Database: PDB / ID: 3f8n
TitleCrystal structure of PerR-Zn-Mn
ComponentsPeroxide operon regulator
KeywordsDNA BINDING PROTEIN / helix-turn-helix / Cytoplasm / DNA-binding / Manganese / Oxidation / Repressor / Transcription / Transcription regulation / Zinc
Function / homology
Function and homology information


regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytoplasm
Similarity search - Function
Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / 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 / 2-Layer Sandwich ...Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Peroxide operon regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsTraore, D.A.K. / Ferrer, J.-L. / Jacquamet, L. / Duarte, V. / Latour, J.-M.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding
Authors: Jacquamet, L. / Traore, D.A.K. / Ferrer, J.-L. / Proux, O. / Testemale, D. / Hazemann, J.-L. / Nazarenko, E. / El Ghazouani, A. / Caux-Thang, C. / Duarte, V. / Latour, J.-M.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Peroxide operon regulator
B: Peroxide operon regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1386
Polymers32,8972
Non-polymers2414
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-21 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.300, 63.340, 66.730
Angle α, β, γ (deg.)90.00, 80.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22A
13A
23B
14A
24B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUARGARGAA6 - 836 - 83
21LEULEUARGARGBB6 - 836 - 83
12ALAALAVALVALBB94 - 10394 - 103
22ALAALAVALVALAA94 - 10394 - 103
13GLUGLUGLYGLYAA114 - 122114 - 122
23GLUGLUGLYGLYBB114 - 122114 - 122
14VALVALVALVALAA125 - 135125 - 135
24VALVALVALVALBB125 - 135125 - 135

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Peroxide operon regulator / PerR


Mass: 16448.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: perR / Plasmid: pET-30c(NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P71086
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 1000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 6901 / Num. obs: 6880 / % possible obs: 99.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rsym value: 0.105 / Net I/σ(I): 11.8
Reflection shellResolution: 3.15→3.4 Å / Redundancy: 3.68 % / Mean I/σ(I) obs: 3.63 / Num. measured all: 1224 / Num. unique all: 1222 / Rsym value: 0.399 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FE3

2fe3


Resolution: 3.15→45.64 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.835 / SU B: 34.028 / SU ML: 0.602 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R Free: 0.567 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; REMARK 500 SHOWS GEOMETRIC DISTORTIONS FOR SOME RESIDUES THAT ARE ALSO LISTED IN REMARK 480. BUT SINCE THEY HAVE BEEN ASSIGNED WITH ZERO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; REMARK 500 SHOWS GEOMETRIC DISTORTIONS FOR SOME RESIDUES THAT ARE ALSO LISTED IN REMARK 480. BUT SINCE THEY HAVE BEEN ASSIGNED WITH ZERO OCCUPANCY, REMARK 500 CAN BE IGNORED FOR THEM.
RfactorNum. reflection% reflectionSelection details
Rfree0.31494 354 5 %RANDOM
Rwork0.27454 ---
all0.27667 6725 --
obs0.27667 6725 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.421 Å2
Baniso -1Baniso -2Baniso -3
1--3.87 Å20 Å20.68 Å2
2--7.73 Å20 Å2
3----4.09 Å2
Refinement stepCycle: LAST / Resolution: 3.15→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 4 1 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212165
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9312943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5755271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83123.774106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.82315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7721511
X-RAY DIFFRACTIONr_chiral_restr0.1180.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021683
X-RAY DIFFRACTIONr_nbd_refined0.2990.21078
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.28
X-RAY DIFFRACTIONr_mcbond_it0.5971.51376
X-RAY DIFFRACTIONr_mcangle_it1.08722163
X-RAY DIFFRACTIONr_scbond_it0.6993869
X-RAY DIFFRACTIONr_scangle_it1.1814.5780
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A304tight positional0.050.05
2B36tight positional0.050.05
3A36tight positional0.040.05
4A40tight positional0.030.05
1A271loose positional0.455
2B23loose positional0.55
3A28loose positional0.485
4A43loose positional0.535
1A304tight thermal4.790.5
2B36tight thermal4.110.5
3A36tight thermal5.670.5
4A40tight thermal2.110.5
1A271loose thermal4.6310
2B23loose thermal4.2210
3A28loose thermal5.4910
4A43loose thermal1.910
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 24 -
Rwork0.372 466 -
obs--100 %

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