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- PDB-6hsd: Crystal structure of the oxidized form of the transcription regul... -

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Basic information

Entry
Database: PDB / ID: 6hsd
TitleCrystal structure of the oxidized form of the transcription regulator RsrR
ComponentsRrf2 family transcriptional regulator
KeywordsTRANSCRIPTION / REDOX SENSOR / IRON SULFUR CLUSTER
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / DNA-binding transcription factor activity / metal ion binding / cytosol
Similarity search - Function
Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Rrf2 family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Crystal Structure of the Transcription Regulator RsrR Reveals a [2Fe-2S] Cluster Coordinated by Cys, Glu, and His Residues.
Authors: Volbeda, A. / Martinez, M.T.P. / Crack, J.C. / Amara, P. / Gigarel, O. / Munnoch, J.T. / Hutchings, M.I. / Darnault, C. / Le Brun, N.E. / Fontecilla-Camps, J.C.
History
DepositionSep 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Feb 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.3May 15, 2024Group: 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rrf2 family transcriptional regulator
B: Rrf2 family transcriptional regulator
C: Rrf2 family transcriptional regulator
D: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,19327
Polymers69,5444
Non-polymers2,64923
Water8,701483
1
A: Rrf2 family transcriptional regulator
C: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,47017
Polymers34,7722
Non-polymers1,69915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-87 kcal/mol
Surface area14580 Å2
MethodPISA
2
B: Rrf2 family transcriptional regulator
D: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,72310
Polymers34,7722
Non-polymers9518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-89 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.290, 94.510, 99.940
Angle α, β, γ (deg.)90.000, 93.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Rrf2 family transcriptional regulator


Mass: 17385.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Gene: SVEN_6563 / Plasmid: pGS-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2RGC9

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Non-polymers , 5 types, 506 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: NaCl, PEG6000, MES, anaerobic

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.945
SYNCHROTRONESRF ID23-121.73978
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 S 6M1PIXELJun 27, 2016
DECTRIS PILATUS3 S 6M2PIXELJun 27, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9451
21.739781
ReflectionResolution: 1.6→47.26 Å / Num. obs: 87187 / % possible obs: 98.6 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.024 / Rrim(I) all: 0.047 / Net I/σ(I): 19.5 / Num. measured all: 332569 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.663.91.43684130.3750.8281.66296.7
6.2-47.263.60.02515370.9990.0150.02998

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→47.26 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.478 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.08
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 4156 4.8 %RANDOM
Rwork0.1403 ---
obs0.1426 82904 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.52 Å2 / Biso mean: 38.807 Å2 / Biso min: 18.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.59 Å2
2---0.06 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.6→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 156 485 5309
Biso mean--48.24 50.55 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135035
X-RAY DIFFRACTIONr_bond_other_d0.0210.0174872
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.646848
X-RAY DIFFRACTIONr_angle_other_deg1.9131.57111270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.695668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.42420.603199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18415746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.241537
X-RAY DIFFRACTIONr_chiral_restr0.0770.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025535
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02956
X-RAY DIFFRACTIONr_rigid_bond_restr4.77739907
X-RAY DIFFRACTIONr_sphericity_free24.6675327
X-RAY DIFFRACTIONr_sphericity_bonded17.459958
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 354 -
Rwork0.329 5836 -
all-6190 -
obs--94.66 %

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