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- PDB-7dvu: Crystal structure of heme sensor protein PefR in complex with hem... -

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Basic information

Entry
Database: PDB / ID: 7dvu
TitleCrystal structure of heme sensor protein PefR in complex with heme and cyanide
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / HTH marR-type domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serotype III
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,4603
Polymers17,8181
Non-polymers6432
Water30617
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)36,9216
Polymers35,6362
Non-polymers1,2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area6240 Å2
ΔGint-64 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.837, 31.390, 77.397
Angle α, β, γ (deg.)90.000, 96.810, 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-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12%(w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl

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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: May 16, 2018 / 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: 2.1→38.46 Å / Num. obs: 19032 / % possible obs: 99.7 % / Redundancy: 6.438 % / Biso Wilson estimate: 62.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Χ2: 1.15 / Net I/σ(I): 14.36 / Num. measured all: 122519
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.226.5440.7691.6130340.9220.83698.7
2.22-2.386.2610.5062.6829080.9550.55399.9
2.38-2.576.3530.3024.5726890.9730.3399.7
2.57-2.816.6820.1728.524530.9920.18699.9
2.81-3.146.4730.10314.9622790.9960.11299.9
3.14-3.626.2750.06424.4619540.9980.0799.7
3.62-4.436.4760.04536.0816840.9990.04999.9
4.43-6.226.4040.03939.5113070.9990.042100
6.22-38.466.4880.03545.757240.9990.03899

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Processing

Software
NameVersionClassification
XSCALENov 11, 2017data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
Coot0.8model building
REFMAC5.8.0258phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DVR

7dvr


Resolution: 2.1→38.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 16.081 / SU ML: 0.195 / SU R Cruickshank DPI: 0.2504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 463 4.6 %RANDOM
Rwork0.2264 ---
obs0.2287 9530 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.72 Å2 / Biso mean: 68.901 Å2 / Biso min: 37.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å2-1.89 Å2
2--1.93 Å20 Å2
3----2.3 Å2
Refinement stepCycle: final / Resolution: 2.1→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 45 17 1216
Biso mean--73.69 59.8 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121247
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.7111685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23222.28157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85915257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.646157
X-RAY DIFFRACTIONr_chiral_restr0.1120.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02899
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 40 -
Rwork0.389 660 -
all-700 -
obs--99.57 %
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)
12.99270.5943.74940.54711.7517.0645-0.0359-0.1767-0.07140.1385-0.17030.10420.2732-0.54810.20630.1948-0.0408-0.09010.1124-0.01530.1618.12556.888771.1337
22.6037-1.7047-0.43651.63340.30123.3262-0.061-0.35220.18890.0846-0.0913-0.1353-0.10460.23160.15220.0725-0.0473-0.11090.31540.02380.179534.52384.479851.4172
32.6835-1.21110.24842.39130.80810.50610.1149-0.0734-0.21330.017-0.13480.01430.0074-0.07860.01990.06530.005-0.12540.27230.04220.254632.3921-2.419543.9133
40.5185-0.4936-1.1311.15752.66526.2303-0.08870.1860.0694-0.0491-0.08580.0739-0.1591-0.16730.17450.10210.0061-0.09920.2118-0.03750.141517.985414.455357.5027
56.7754-2.18444.53672.6238-3.18154.6045-0.17990.2247-0.1252-0.1908-0.1373-0.34090.02010.22930.31720.2863-0.0275-0.09630.06240.04320.189432.029221.552175.7594
611.2298-4.51254.88029.14093.39356.0339-0.03260.27620.2391-0.00480.2924-0.5863-0.02510.4226-0.25970.0529-0.0129-0.06010.1477-0.03480.183824.937416.603862.6096
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 - 142

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