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- PDB-7dvr: Crystal structure of heme sensor protein PefR from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 7dvr
TitleCrystal structure of heme sensor protein PefR from Streptococcus agalactiae in complex with heme
ComponentsHTH marR-type domain-containing protein
KeywordsTRANSCRIPTION / heme-binding / helix-turn-helix
Function / homology
Function and homology information


DNA-binding transcription factor activity / metal ion binding
Similarity search - Function
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
: / PROTOPORPHYRIN IX CONTAINING FE / HTH marR-type domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serotype III
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
Model detailsheme sensor protein
AuthorsNishinaga, M. / Nagai, S. / Nishitani, Y. / Sugimoto, H. / Shiro, Y. / Sawai, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26220807 Japan
Japan Society for the Promotion of Science (JSPS)JP18H02396 Japan
Japan Society for the Promotion of Science (JSPS)JP18K05321 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Authors: Nishinaga, M. / Sugimoto, H. / Nishitani, Y. / Nagai, S. / Nagatoishi, S. / Muraki, N. / Tosha, T. / Tsumoto, K. / Aono, S. / Shiro, Y. / Sawai, H.
History
DepositionJan 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH marR-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4933
Polymers17,8181
Non-polymers6752
Water66737
1
A: HTH marR-type domain-containing protein
hetero molecules

A: HTH marR-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9876
Polymers35,6362
Non-polymers1,3514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5920 Å2
ΔGint-70 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.899, 32.149, 76.654
Angle α, β, γ (deg.)90.000, 95.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HTH marR-type domain-containing protein


Mass: 17817.852 Da / Num. of mol.: 1 / Fragment: heme sensor protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serotype III (strain NEM316) (bacteria)
Strain: NEM316 / Gene: gbs1402 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E4J9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35%(v/v) MPD, 0.2 M KCl, 50 mM hexamine cobalt(III) chloride, 50 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2017 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→29.13 Å / Num. obs: 18070 / % possible obs: 97.1 % / Redundancy: 6.591 % / Biso Wilson estimate: 51.157 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.054 / Χ2: 1.094 / Net I/σ(I): 16.27 / Num. measured all: 119107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.86.9890.9541.4719890298128460.8531.0395.5
1.8-1.936.7780.3753.618157277726790.9760.40696.5
1.93-2.086.8370.1768.0317244260825220.9950.1996.7
2.08-2.286.9040.10714.8516169240823420.9960.11697.3
2.28-2.546.4060.07321.6713683218721360.9970.07997.7
2.54-2.936.2950.05728.412011195019080.9980.06297.8
2.93-3.585.9930.0532.79553162215940.9980.05598.3
3.58-5.036.0820.04335.47773129612780.9980.04798.6
5.03-29.136.0480.04635.6646277857650.9980.0597.5

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength111.7385-4
3 wavelength121.73853-8
3 wavelength131.723.5-1
Phasing MAD set siteAtom type symbol: Fe / B iso: 12.836 / Fract x: 0.037 / Fract y: 0 / Fract z: 0.177 / Occupancy: 0.511
Phasing dmFOM : 0.72 / FOM acentric: 0.72 / FOM centric: 0.67 / Reflection: 3804 / Reflection acentric: 3336 / Reflection centric: 468
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.9-19.590.930.940.9219613759
4.9-7.90.830.850.7260450599
3.9-4.90.860.880.7573463797
3.5-3.90.780.790.6871764176
3-3.50.590.60.511921092100
2.8-30.410.410.436132437

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Processing

Software
NameVersionClassification
XSCALEJun 1, 2017data scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSJun 1, 2017data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.3196 / WRfactor Rwork: 0.2751 / FOM work R set: 0.6971 / SU B: 9.635 / SU ML: 0.145 / SU R Cruickshank DPI: 0.1361 / SU Rfree: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 882 4.9 %RANDOM
Rwork0.2366 ---
obs0.2386 17175 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.55 Å2 / Biso mean: 50.487 Å2 / Biso min: 33.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-1.32 Å2
2--1.22 Å20 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 1.7→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 44 37 1277
Biso mean--65.35 55.04 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171255
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.7121742
X-RAY DIFFRACTIONr_angle_other_deg1.4661.6172917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9735152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70322.62361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.646157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021391
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02258
LS refinement shellResolution: 1.704→1.748 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 63 -
Rwork0.531 1213 -
all-1276 -
obs--94.17 %
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)
12.4396-0.02732.60470.0843-0.70718.5747-0.1008-0.12710.09980.02440.00210.0136-0.119-0.31430.09860.22510.0144-0.0010.1733-0.02080.333320.19197.379871.0601
20.5381-0.0355-0.74680.1552-0.44522.7172-0.0147-0.21550.00450.0461-0.0591-0.0167-0.14780.33640.07380.01630.00880.01340.51240.03120.292936.09394.152951.0913
33.5995-2.0190.03971.32420.53341.8629-0.0748-0.0947-0.13880.0132-0.01940.0462-0.0670.0530.09410.01240.00410.05240.39230.07460.345333.6187-2.766843.7417
40.3738-1.065-1.3223.35694.40877.2892-0.06470.17710.03330.1776-0.2133-0.022-0.2676-0.10380.2780.2022-0.0297-0.03850.35920.02430.281820.003714.923556.8895
54.7113-1.09023.94433.6071-3.40515.7936-0.10680.6272-0.298-0.1352-0.1818-0.2741-0.06880.80320.28860.4537-0.0945-0.02440.20980.00690.371935.907420.711375.1811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2A31 - 70
3X-RAY DIFFRACTION3A71 - 100
4X-RAY DIFFRACTION4A101 - 121
5X-RAY DIFFRACTION5A122 - 147

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