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- PDB-7cbv: Crystal structure of the transcriptional regulator PadR from Baci... -

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Basic information

Entry
Database: PDB / ID: 7cbv
TitleCrystal structure of the transcriptional regulator PadR from Bacillus subtilis (space group H32)
ComponentsPadR family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor
Function / homologyTranscription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / PadR family transcriptional regulator
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPark, S.C. / Song, W.S. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Apo structure of the transcriptional regulator PadR from Bacillus subtilis: Structural dynamics and conserved Y70 residue.
Authors: Park, S.C. / Song, W.S. / Yoon, S.I.
History
DepositionJun 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PadR family transcriptional regulator
B: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water1,17165
1
A: PadR family transcriptional regulator

A: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area6780 Å2
ΔGint-50 kcal/mol
Surface area16490 Å2
MethodPISA
2
B: PadR family transcriptional regulator

B: PadR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,5022
Polymers43,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area6630 Å2
ΔGint-47 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.697, 123.697, 182.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(chain 'A' and ((resid 2 and (name N or name...AA2 - 578 - 63
12LYSLYSSERSER(chain 'A' and ((resid 2 and (name N or name...AA68 - 10974 - 115
13GLNGLNMETMET(chain 'A' and ((resid 2 and (name N or name...AA111 - 139117 - 145
14PROPROASPASP(chain 'A' and ((resid 2 and (name N or name...AA144 - 180150 - 186
25ARGARGARGARG(chain 'B' and (resid 2 through 46 or (resid 47...BB2 - 578 - 63
26LYSLYSSERSER(chain 'B' and (resid 2 through 46 or (resid 47...BB68 - 10974 - 115
27GLNGLNMETMET(chain 'B' and (resid 2 through 46 or (resid 47...BB111 - 139117 - 145
28PROPROASPASP(chain 'B' and (resid 2 through 46 or (resid 47...BB144 - 180150 - 186

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Components

#1: Protein PadR family transcriptional regulator / PadR


Mass: 21750.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: FIU26_19465 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5F2KJ26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: polyethylene glycol monomethyl ether 5000, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 23965 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2371 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X12

5x12


Resolution: 2.3→29.33 Å / SU ML: 0.2512 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.0461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2272 1222 5.11 %
Rwork0.195 22704 -
obs0.1966 23926 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.64 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 0 65 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742732
X-RAY DIFFRACTIONf_angle_d0.90213677
X-RAY DIFFRACTIONf_chiral_restr0.0444404
X-RAY DIFFRACTIONf_plane_restr0.006452
X-RAY DIFFRACTIONf_dihedral_angle_d11.10161633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.28421310.24352526X-RAY DIFFRACTION99.77
2.39-2.50.26671220.2242503X-RAY DIFFRACTION99.85
2.5-2.630.27171380.22942518X-RAY DIFFRACTION99.74
2.63-2.80.2611430.21672504X-RAY DIFFRACTION99.77
2.8-3.010.25371560.22012508X-RAY DIFFRACTION99.55
3.01-3.320.28861480.21092502X-RAY DIFFRACTION99.55
3.32-3.80.19421510.18722523X-RAY DIFFRACTION99.15
3.8-4.780.19281170.16262535X-RAY DIFFRACTION98.22
4.78-29.330.19221160.18062585X-RAY DIFFRACTION96.26
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)
13.3750655225-0.114662908423-0.03849451671094.103957237610.4902525321421.80383474423-0.06371336063040.5013268556560.461275974934-0.6359360809810.07893432609350.426609812658-0.219087833146-0.1869854562360.003641743366410.284953795898-0.00739827673855-0.07526754195250.3247215053960.08652823444430.352348801706-11.687166024814.042402574322.4837346752
25.18167479511-1.613462628022.869797183330.998592256725-0.4090045901191.94667300588-0.465042553438-0.2780835480870.3186859800670.401086830982-0.0706432506669-0.210131035359-0.493996637027-0.06928664388120.4411135250710.35273414196-0.0281103215436-0.0338131404870.570942422177-0.09424726375030.475948547294-27.078335396212.63470834237.230374446
32.77743211944-1.643603860410.213907721631.906136140890.3367598682571.586702688830.1318694326590.475854822538-0.197150683335-0.194442869388-0.119771286310.2035702706030.1234021788940.06154883515220.01421022434640.2190897997550.00254105461927-0.03074850521510.247244634829-0.03769768943360.232530233468-44.982779005612.802743062823.2586210327
42.71646075209-1.369947996480.337079095311.46699827879-0.6213351490710.7544898224980.2174142903620.525982797717-0.541758222926-0.205528739338-0.2636426507560.2349192660160.160344012262-0.05955490918360.04475160975920.248402554533-0.00222157620279-0.02726878606090.262039072612-0.08300512306630.294031433681-36.07151580632.4283521397724.7977896502
54.03036102158-0.901285863918-0.1512244420743.28194677641-1.247070908722.79212568268-0.0252040186517-1.019245478460.6170762188190.3342244747110.1053116808640.3207877842840.217881274818-0.768085977503-0.03143642767350.592145834544-0.2351934111880.09271207785430.852227310961-0.1585654856860.642605420933-65.2065930774-18.90634540728.97723304567
60.6738139869330.3419912983280.5769733262485.951001897672.706817590732.284545412410.1698879761210.211296501805-0.545139138088-0.510357119131-0.4692141880090.5164867157270.280531646207-0.3257767690660.1282943896140.476542673042-0.0983520910998-0.07236767944110.545672703666-0.1778852977530.557946974298-56.3795275129-6.93995978328-6.52172844929
70.751436780886-0.3187738209040.5454079639541.84669016536-0.2368199191472.215777632770.114125657219-0.0651808643330.569116703757-0.291345782391-0.508370079990.232475533334-1.21592946456-0.3950271696070.5496357018460.6402321736720.158740403057-0.1338813180290.359344033749-0.02566284634450.449874552114-53.031070387417.1664843647-3.25510700026
82.052653653540.09855864054760.2667960576995.84323607787-0.2601542110695.07723250912-0.0619356883262-0.1786166154470.1983600666430.716085448604-0.00844522049201-0.162198972878-0.320768146204-0.03192604617180.06799821229630.2940840558760.015783511354-0.058737329730.295179652292-0.09484530840290.250450464097-45.5499624958.2015478426310.2213793455
91.48147077270.1667004020880.1504211020864.121038872381.049766853493.1678011366-0.0668075443682-0.140830571255-0.1247296415540.5025120111960.196782748379-0.3349705240680.3414252101170.108368109209-0.04503332320660.3100096729060.0228937786541-0.05877449692440.29402955341-0.06572934240490.321721046919-43.0303446127-3.035056704276.24348381091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 85 )
6X-RAY DIFFRACTION6chain 'B' and (resid 86 through 96 )
7X-RAY DIFFRACTION7chain 'B' and (resid 97 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 138 )
9X-RAY DIFFRACTION9chain 'B' and (resid 139 through 180 )

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