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- PDB-7t8o: Crystal Structure of the Crp/Fnr Family Transcriptional Regulator... -

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Basic information

Entry
Database: PDB / ID: 7t8o
TitleCrystal Structure of the Crp/Fnr Family Transcriptional Regulator from Listeria monocytogenes
ComponentsLmo0753 protein
KeywordsTRANSCRIPTION / Transcriptional regulator / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Shatsman, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Crp/Fnr Family Transcriptional Regulator from Listeria monocytogenes
Authors: Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Shatsman, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0753 protein
B: Lmo0753 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5043
Polymers52,4082
Non-polymers961
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-38 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.091, 76.308, 171.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Lmo0753 protein


Mass: 26204.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0753 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8Y8Y9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium Sulfate, 0.1 M Tris HKL pH 8.5, 20 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15776 / % possible obs: 91.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 55.37 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.189 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 545 / CC1/2: 0.6 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.71→45.75 Å / SU ML: 0.4261 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.4387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 735 4.69 %
Rwork0.2506 14940 -
obs0.2523 15675 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.1 Å2
Refinement stepCycle: LAST / Resolution: 2.71→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 5 0 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243632
X-RAY DIFFRACTIONf_angle_d0.43674909
X-RAY DIFFRACTIONf_chiral_restr0.0427578
X-RAY DIFFRACTIONf_plane_restr0.0035627
X-RAY DIFFRACTIONf_dihedral_angle_d16.06521378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.920.43081050.35292236X-RAY DIFFRACTION70.09
2.92-3.210.37981340.32122763X-RAY DIFFRACTION85.91
3.21-3.670.34261680.28793210X-RAY DIFFRACTION99.27
3.67-4.630.25521590.2293294X-RAY DIFFRACTION99.94
4.63-45.750.23981690.21563437X-RAY DIFFRACTION99.7
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)
14.323832161361.041885862560.3562497500223.202634519040.07870486494974.43119411876-0.005282888296040.0812838644652-0.0971634484074-0.165904482270.122634551881-0.245172273967-0.2641940927160.432331867935-0.2319384841130.290481406411-0.0544714117163-0.0246513562490.3516538999330.001748763402440.3990233871815.28460897499-3.2717898565743.4186201517
23.658787526291.68061850813-0.8009480252494.366372319761.59402783433.39580476255-0.2059016346040.47577106607-0.3209941904780.3071598225370.0828178018929-0.134250596978-0.0776313466903-0.543786299773-0.1249675170880.254318658936-0.0308213568178-0.02018108065090.307630393782-0.04089722251510.337344098629-0.882178538976-8.6758254991245.6060092013
32.00426959197-0.529774277206-3.158427986321.11195077108-0.8120628104187.725935647020.957788045758-0.1089137361270.3985529063210.0200322271591-0.474799859007-0.415961776157-1.000033174871.1506267521-0.7064689891090.680192104966-0.229935764541-0.1693193731450.909184400779-0.01814239285570.522404400243-5.29038239769-6.8374970022522.8137253711
43.5091068069-0.7961031578060.5643632549983.16555383680.4614305280933.447154923270.05688477108440.1286162290770.04228744498250.0762693916994-0.1823503896530.0960984672517-0.4707254332130.3522931168350.1126363484230.463849341471-0.03038551533190.06572145293390.4199052630540.06842920258050.328007485491-3.20599133841-6.29755361199-0.0528415316181
53.122108805860.469164192690.4903732884862.94179019789-0.1738981069954.336549524470.076205036003-0.303007957342-0.4351244690030.4019652615210.03394433608170.04679064662780.126061781692-0.21436986201-0.1148577449290.359631602327-0.06528916440750.066409023060.35307555365-0.0157217992050.380462885486-21.1754698693-23.604362275652.2143118716
64.550973475710.9725464870272.638036180710.3614684625160.3519508639824.67652199531-0.0566419032394-0.6239491764950.3683698736350.30835746019-0.230718279540.128811418494-0.327739163151-0.5246396373310.2726221793660.443316979651-0.06695303230310.007590178663960.2881689589630.03077641557110.426006540426-15.9652667335-16.500113771351.0478596652
74.142189161-0.0083395442446-0.9504061490631.796593133551.986341829033.488013581040.0162283768009-0.3447267139120.2634232183090.170776248340.140952748351-0.162189233876-0.245301520801-0.181164284763-0.1351135884920.3559322598970.0301137366784-0.006017071147650.4037925461210.045849563580.227541090611-13.8482780785-19.740824357715.3460561939
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 71 )AA-1 - 711 - 73
22chain 'A' and (resid 72 through 141 )AA72 - 14174 - 143
33chain 'A' and (resid 142 through 155 )AA142 - 155144 - 157
44chain 'A' and (resid 156 through 221 )AA156 - 221158 - 223
55chain 'B' and (resid 2 through 83 )BB2 - 831 - 82
66chain 'B' and (resid 84 through 143 )BB84 - 14383 - 142
77chain 'B' and (resid 144 through 225 )BB144 - 225143 - 224

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