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- PDB-9ff3: The structure of delta-ScoC, a global regulator protein from Geob... -

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Basic information

Entry
Database: PDB / ID: 9ff3
TitleThe structure of delta-ScoC, a global regulator protein from Geobacillus kaustophilus T-1
ComponentsHTH-type transcriptional regulator Hpr
KeywordsDNA BINDING PROTEIN / ScoC / Global regulator / Geobacillus kaustophilus / Tetramer / DNA bending / Hpr
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / response to stress / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional regulator Hpr / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator Hpr
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsHadad, N. / Shulami, S. / Pomyalov, S. / Shoham, Y. / Shoham, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation500/10 Israel
CitationJournal: To Be Published
Title: The structure of delta-ScoC, a global regulator protein from Geobacillus kaustophilus T-1
Authors: Hadad, N. / Shulami, S. / Pomyalov, S. / Shoham, Y. / Shoham, G.
History
DepositionMay 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HTH-type transcriptional regulator Hpr


Theoretical massNumber of molelcules
Total (without water)24,5851
Polymers24,5851
Non-polymers00
Water21612
1
C: HTH-type transcriptional regulator Hpr

C: HTH-type transcriptional regulator Hpr

C: HTH-type transcriptional regulator Hpr

C: HTH-type transcriptional regulator Hpr


Theoretical massNumber of molelcules
Total (without water)98,3414
Polymers98,3414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area16650 Å2
ΔGint-136 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.082, 80.082, 164.149
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11C-311-

HOH

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Components

#1: Protein HTH-type transcriptional regulator Hpr / Protease production regulatory protein Hpr


Mass: 24585.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: hpr, GK0652 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L293
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4% PEG 4K, 0.1M Sodium acetate, and 8% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.32→38.9 Å / Num. obs: 5080 / % possible obs: 99.7 % / Redundancy: 19.5 % / Biso Wilson estimate: 101.52 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.026 / Rrim(I) all: 0.11 / Net I/σ(I): 19.1
Reflection shellResolution: 3.32→3.43 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 992 / CC1/2: 0.94 / Rpim(I) all: 0.62 / Rrim(I) all: 0.59

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→38.9 Å / SU ML: 0.3705 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2846 395 7.83 %
Rwork0.2487 4651 -
obs0.2516 5046 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.45 Å2
Refinement stepCycle: LAST / Resolution: 3.32→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 0 12 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411486
X-RAY DIFFRACTIONf_angle_d0.62281994
X-RAY DIFFRACTIONf_chiral_restr0.038207
X-RAY DIFFRACTIONf_plane_restr0.0047252
X-RAY DIFFRACTIONf_dihedral_angle_d14.1334185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.790.32421310.26311476X-RAY DIFFRACTION99.32
3.79-4.780.27851240.2591529X-RAY DIFFRACTION100
4.78-38.90.27631400.23861646X-RAY DIFFRACTION99.78
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.243727296820.4027581364860.5911084702080.221632219142-0.2248880291871.500813013480.3330646855530.7934171226631.278206316741.01221649495-0.4556186626310.4912567466150.8717825335830.433872731147-0.3127010564361.6379911410.6908928476120.5205109147740.1499897539420.2187649996871.0316066287310.8130421739-17.6771429017-24.1650698509
20.4881462192840.0666349336197-0.1192013018422.17700188681.619803624541.27898347292-0.0579557056925-0.264726381662-0.0005955708767970.9182505275090.0816509718505-0.3901936751290.5545355471060.2763476745790.02151165441782.14098651460.5013411319170.5566412036440.7486618668550.0376447852940.7114260487986.83475533867-30.6277657439-12.7606689609
31.52129297131-0.486824087596-0.5738709604531.026939257210.3076086381890.813286747610.174990957803-0.1649043068350.2064931343490.16026576124-0.175869990185-0.3829025815350.4947270672050.1028616425410.07961069140852.519260919941.07663348311.17091300262-0.100664909859-0.7617459031930.2788031893842.92404255776-34.0089230287-3.79026445207
43.11913480983-1.382287000182.93849133261.62365759192-2.122642954853.52301228258-0.4438795993110.1398587790851.649754696990.823652110836-0.622126919070.09163541381830.429828210252-0.4772288075610.5685321019751.003644401310.2536476877560.653062347750.605390787208-0.08355036424341.4570086068216.4977288995-7.86519523571-13.0496344915
50.165989238262-0.2109831399010.004908867566960.264530071869-0.003705222786230.42685418971-0.31860575591-0.3398236726150.3252514896920.288270411945-0.1052954379920.0771049956339-0.2744710346020.239759284282-0.1511580467541.388715149730.5780115934980.887306687630.161067809758-0.2412668589042.04683321579-0.00577797933742-11.6169665934-17.055252346
61.35442380582-1.266444493151.658869375873.153157523570.8278752572967.331737040430.610945607309-1.525284552540.1610872448041.58412161389-0.7589842668110.112315665031-0.4169678755510.065648721227-0.06526527594282.067989166630.0009358976775010.0264222562761.17658015107-0.604621121851.4415502583713.9285952649-8.20031267796-0.194112121112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 7 through 57 )
2X-RAY DIFFRACTION2chain 'C' and (resid 58 through 87 )
3X-RAY DIFFRACTION3chain 'C' and (resid 88 through 109 )
4X-RAY DIFFRACTION4chain 'C' and (resid 110 through 139 )
5X-RAY DIFFRACTION5chain 'C' and (resid 140 through 172 )
6X-RAY DIFFRACTION6chain 'C' and (resid 173 through 180 )

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