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- PDB-5dl2: Crystal Structure of RopB -

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Basic information

Entry
Database: PDB / ID: 5dl2
TitleCrystal Structure of RopB
ComponentsRegulator of protease B (RopB)
KeywordsTRANSCRIPTION REGULATOR / virulence / virulence regulation / Tetratricopeptide repeat / Bacterial pathogenesis
Function / homologyTranscription activator MutR, C-terminal / HTH-type transcriptional regulator Rgg, C-terminal domain / : / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / DNA binding / Putative transcription regulator
Function and homology information
Biological speciesStreptococcus pyogenes MGAS10870 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKumaraswami, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI103708-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109096-01A1 United States
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structural and functional analysis of RopB: a major virulence regulator in Streptococcus pyogenes.
Authors: Makthal, N. / Gavagan, M. / Do, H. / Olsen, R.J. / Musser, J.M. / Kumaraswami, M.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of protease B (RopB)
B: Regulator of protease B (RopB)


Theoretical massNumber of molelcules
Total (without water)55,9562
Polymers55,9562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-13 kcal/mol
Surface area25660 Å2
MethodPISA
2
A: Regulator of protease B (RopB)
B: Regulator of protease B (RopB)

A: Regulator of protease B (RopB)
B: Regulator of protease B (RopB)


Theoretical massNumber of molelcules
Total (without water)111,9134
Polymers111,9134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area9050 Å2
ΔGint-77 kcal/mol
Surface area46160 Å2
MethodPISA
3
A: Regulator of protease B (RopB)

B: Regulator of protease B (RopB)


Theoretical massNumber of molelcules
Total (without water)55,9562
Polymers55,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
Buried area1040 Å2
ΔGint-10 kcal/mol
Surface area26570 Å2
MethodPISA
4
A: Regulator of protease B (RopB)

A: Regulator of protease B (RopB)


Theoretical massNumber of molelcules
Total (without water)55,9562
Polymers55,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area2220 Å2
ΔGint-24 kcal/mol
Surface area25490 Å2
MethodPISA
5
B: Regulator of protease B (RopB)

B: Regulator of protease B (RopB)


Theoretical massNumber of molelcules
Total (without water)55,9562
Polymers55,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area2230 Å2
ΔGint-24 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.060, 94.060, 178.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Regulator of protease B (RopB) / Putative transcription regulator


Mass: 27978.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS10870 (bacteria)
Strain: MGAS10870 / Gene: rgg / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3KVD8

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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: 4.07 Å3/Da / Density % sol: 69.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Potassium formate, PEG2000, potassium chloride, Tris-HCl
PH range: 8 - 8.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→81 Å / Num. all: 13475 / Num. obs: 13475 / % possible obs: 97.4 % / Redundancy: 5.4 % / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→81 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3134 1126 9.97 %
Rwork0.2757 --
obs0.2796 11298 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 0 0 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043776
X-RAY DIFFRACTIONf_angle_d0.8655080
X-RAY DIFFRACTIONf_dihedral_angle_d15.6271390
X-RAY DIFFRACTIONf_chiral_restr0.035564
X-RAY DIFFRACTIONf_plane_restr0.004638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5002-3.65950.42361360.35521237X-RAY DIFFRACTION97
3.6595-3.85250.43741410.32861248X-RAY DIFFRACTION97
3.8525-4.09380.40461360.29711283X-RAY DIFFRACTION97
4.0938-4.40990.29521390.26371243X-RAY DIFFRACTION97
4.4099-4.85360.27481390.22371260X-RAY DIFFRACTION97
4.8536-5.55580.34451440.28241281X-RAY DIFFRACTION97
5.5558-6.99920.39331450.35071280X-RAY DIFFRACTION98
6.9992-81.48030.24581460.24751340X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 43.6237 Å / Origin y: -16.0132 Å / Origin z: 2.3079 Å
111213212223313233
T1.1322 Å2-0.1755 Å20.1461 Å2-1.3476 Å20.0091 Å2--1.1097 Å2
L1.5185 °20.9837 °21.0966 °2-1.1463 °20.5219 °2--2.6519 °2
S0.2397 Å °-0.0533 Å °0.1538 Å °0.3348 Å °-0.1227 Å °0.145 Å °-0.5488 Å °-0.3953 Å °-0.1097 Å °
Refinement TLS groupSelection details: all

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