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- PDB-4lmy: Structure of GAS PerR-Zn-Zn -

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Basic information

Entry
Database: PDB / ID: 4lmy
TitleStructure of GAS PerR-Zn-Zn
ComponentsPeroxide stress regulator PerR, FUR family
KeywordsTRANSCRIPTION / Transcription Factor / Zinc Binding
Function / homologyFerric-uptake regulator, C-terminal dimerisarion domain / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLin, C.S. / Chao, S.Y. / Nix, J.C. / Tseng, H.L. / Tsou, C.C. / Fei, C.H. / Ciou, H.S. / Jeng, U.S. / Lin, Y.S. / Chuang, W.J. ...Lin, C.S. / Chao, S.Y. / Nix, J.C. / Tseng, H.L. / Tsou, C.C. / Fei, C.H. / Ciou, H.S. / Jeng, U.S. / Lin, Y.S. / Chuang, W.J. / Wu, J.J. / Wang, S.
CitationJournal: Plos One / Year: 2014
Title: Distinct structural features of the peroxide response regulator from group a streptococcus drive DNA binding
Authors: Lin, C.S. / Chao, S.Y. / Hammel, M. / Nix, J.C. / Tseng, H.L. / Tsou, C.C. / Fei, C.H. / Chiou, H.S. / Jeng, U.S. / Lin, Y.S. / Chuang, W.J. / Wu, J.J. / Wang, S.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_ref_seq_dif / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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 stress regulator PerR, FUR family
B: Peroxide stress regulator PerR, FUR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0606
Polymers37,7992
Non-polymers2624
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-18 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.109, 87.496, 59.389
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxide stress regulator PerR, FUR family


Mass: 18899.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: NS88.2 / Gene: spf / Production host: Escherichia coli (E. coli) / References: UniProt: H8F5Y5
#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.: 185 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1M Tris, 0.25M magnesium chloride, 27% PEG 4000, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONALS 4.2.221.28276, 1.28296, 1.2570
Detector
TypeIDDetectorDate
NOIR-11CCDJul 26, 2009
ADSC QUANTUM 3152CCDMay 23, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.282761
31.282961
41.2571
ReflectionResolution: 1.5→30 Å / Num. all: 54532 / Num. obs: 51675 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 23.66 Å2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.7 % / Num. unique all: 4294 / % possible all: 79.7

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
d*TREKdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→21.169 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8339 / SU ML: 0.18 / σ(F): 1.36 / Phase error: 24.22 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 2180 5.02 %RANDOM
Rwork0.2204 ---
all0.2213 44425 --
obs0.2213 43404 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.1 Å2 / Biso mean: 32.4891 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 4 185 2648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032509
X-RAY DIFFRACTIONf_angle_d0.7893400
X-RAY DIFFRACTIONf_chiral_restr0.057383
X-RAY DIFFRACTIONf_plane_restr0.003442
X-RAY DIFFRACTIONf_dihedral_angle_d13.809933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63480.31911540.28922600275499
1.6348-1.67280.29631580.273226222780100
1.6728-1.71460.2991350.25525932728100
1.7146-1.76090.30011300.261526432773100
1.7609-1.81270.27551440.245626162760100
1.8127-1.87120.24921430.23426052748100
1.8712-1.9380.24861450.227226342779100
1.938-2.01560.27961490.231625782727100
2.0156-2.10720.22921250.220626612786100
2.1072-2.21820.27321290.212726372766100
2.2182-2.3570.24951400.2326492789100
2.357-2.53870.21371550.218126062761100
2.5387-2.79370.24871210.21732628274999
2.7937-3.19680.21811340.22442579271398
3.1968-4.02310.21941010.21672372247388
4.0231-21.17130.22291170.19542201231882

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