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- PDB-7dvs: Crystal structure of Apo (heme-free) PefR -

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Basic information

Entry
Database: PDB / ID: 7dvs
TitleCrystal structure of Apo (heme-free) PefR
ComponentsMarR family transcriptional regulator
KeywordsTRANSCRIPTION / Heme / transcription regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity
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
MarR family transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMuraki, N. / Aono, S.
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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

Downloads & links

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Assembly

Deposited unit
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)75,2394
Polymers75,2394
Non-polymers00
Water00
1
A: MarR family transcriptional regulator
B: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)37,6202
Polymers37,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-28 kcal/mol
Surface area16150 Å2
MethodPISA
2
C: MarR family transcriptional regulator
D: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)37,6202
Polymers37,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-14 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.980, 46.020, 135.220
Angle α, β, γ (deg.)90.000, 92.810, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 3 - 140 / Label seq-ID: 19 - 156

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 3 through 16 or (resid 17...AA
2(chain 'B' and (resid 3 through 47 or (resid 48...BB

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Components

#1: Protein
MarR family transcriptional regulator / Transcriptional regulator / MarR family


Mass: 18809.873 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Gene: AX245_08385, C6N10_09725, DX05_07110, E8E04_04745, F5043_04730, GD434_04460, NCTC6175_00806, RDF_1281
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4Z9I5

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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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% (w/v) polyethylene glycol 4000, 0.2 M magnesium chloride, 0.1 M sodium acetate (pH4.6), 16% (v/v) 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 23177 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 78.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.044 / Net I/σ(I): 18.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1674 / CC1/2: 0.836 / Rrim(I) all: 0.759 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LW6

6lw6
PDB Unreleased entry


Resolution: 2.6→46.59 Å / SU ML: 0.3696 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.4974
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 1157 5 %Random selection
Rwork0.2363 ---
obs0.239 23158 97.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 107.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 0 0 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713767
X-RAY DIFFRACTIONf_angle_d0.88535119
X-RAY DIFFRACTIONf_chiral_restr0.0496620
X-RAY DIFFRACTIONf_plane_restr0.0067647
X-RAY DIFFRACTIONf_dihedral_angle_d15.29432275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.35681440.29492734X-RAY DIFFRACTION97.39
2.72-2.860.41621450.28252750X-RAY DIFFRACTION99.11
2.86-3.040.3131440.27682738X-RAY DIFFRACTION99.11
3.04-3.280.4291480.2852818X-RAY DIFFRACTION99.36
3.28-3.60.29931450.25422756X-RAY DIFFRACTION99.38
3.6-4.130.25431460.20732810X-RAY DIFFRACTION99.36
4.13-5.20.22971490.20492828X-RAY DIFFRACTION99.5
5.2-46.590.30251360.24672567X-RAY DIFFRACTION87.5
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)
13.553903239520.08786439153381.867871565554.54576762087-1.922742614322.29763886384-0.687106297906-0.1904018325280.3868215393370.08322126716220.141109030615-0.119571014703-1.829205084541.506606120870.4394479969460.658533248854-0.174041134635-0.04202768207570.548946831553-0.0189783825980.778467456758134.8923989891.28183265907187.030278804
23.60129746068-3.209536769880.8683720434452.97524318705-1.766295037754.23955625276-0.4306936670870.354252456319-0.702132184587-0.5065469589330.5335939582650.2805214867520.95277492433-0.687447470666-0.08400999863870.880508856194-0.2374632674640.0298451945540.751207855471-0.08746388731130.769912178769116.391607763-3.58009560387171.478701717
31.85823218121-2.49276186705-0.639781743864.4449231465-0.4095293805126.46858175145-0.3185058095240.5509166845960.45102104379-0.2344630486130.4172831847240.254858741741-0.698072649427-0.175676177067-0.1507659694320.750351831733-0.401275391832-0.1229509341770.907790888860.1798118981050.843100448551106.9865937952.46465843198172.871263712
44.39019129081-1.162675939442.520998697522.772365091091.899137532226.9696873377-0.4039304573051.7968288766-0.351338642356-0.653725433780.01551686068350.0371481771591.124451695040.3143343322810.3547448322280.918152394329-0.4053495544780.09899328120920.8993583585160.05831612027010.796367435641126.189445213-4.92808777336170.573469381
53.82130743184-0.193458098029-4.222625713513.0600268001-3.29078658039.02027068135-0.765781502999-0.5142450679530.347700863895-0.3161516954580.681528391685-0.2111894239970.9711480508120.112706930649-0.01647092159370.747270385756-0.0371824356570.004394393194430.657965985183-0.07075119246570.823501256927123.879458818-7.95012149206192.696389645
62.95108298432-0.4883508863241.714926327451.68282161826-2.70267083583.94361362489-0.0299718314853-0.2006545467980.9025753436120.08316624447870.262714881348-0.0337084891919-2.59492575114-1.57036856361-0.5306410835470.8439875549510.0758077616541-0.0635164688420.713562056926-0.03031440004360.947466894103125.3781591574.21406727778203.247349486
77.62613984256-2.15480281339-1.230114756798.86700006813-2.822717438665.761359348620.6710407173761.15023563622-0.468085985122-1.02512736852-0.8055593912841.110174597170.5109170031810.03848110196930.01831648235580.7532223188880.106935011561-0.1126680329280.925942036062-0.08460079038050.824584053616140.482726696-8.58281470434216.871133414
83.93232631137-3.27932281894-0.766423071196.570063450651.373820661676.495956830140.532690602780.6182610932660.0466574058577-1.13557427058-0.655295943881-1.16360949814-0.720104466778-0.02059178083560.09654286102830.7914983927770.09359989427010.03276381038720.7457667161080.1086539109820.776912683312150.649294048-4.33036895065220.031166788
96.266777751180.8315957938531.34308698214-0.696366906954-0.3214666251856.20599666258-0.407517825389-0.6967302245020.03331783185410.02111016680940.2566259839420.2210192517830.0836545535356-1.127032904040.1764917438360.6090286983920.163378066769-0.009335389950090.778410313756-0.03943294776870.78558305865131.105495417-5.96242111299218.813206968
102.86389346743-0.751843322923-4.308266260288.178035550270.9616038892228.40732467957-0.873300857873-0.522090516056-2.3459386224-0.034335910322-0.426794623524-0.1115936755621.30878694810.9630790023271.049498783031.010300093150.03260799516080.1024320849160.663612945920.04382917205690.806440950733131.077896189-11.3272032487194.719627672
112.927411277622.35516168398-2.443572173282.996591541371.017833457459.544148886270.6767028866610.05742505690840.247686899170.0229470912755-0.484595999389-0.156111325947-0.612401107763-0.00155675290822-0.3547562568391.24454147178-0.244141263026-0.03361353743011.612890698050.2633463766760.824517956319136.577672123-7.30671273444153.323675467
126.32993337511.697986383460.2828215255146.76238543930.6531605212896.86961653864-0.5459097082740.969902475777-0.563004127159-0.9658036047340.674231863072-0.2254381544470.247305736852-0.373316637976-0.2104294091850.906531368435-0.2396488190620.1077468318210.84209418761-0.1164369870130.755333670719138.613407632-30.3170603297165.610579435
136.09040631659-4.10810296958-1.591228688174.7025089101-0.5296424687752.983203212560.04051188848920.2493000895950.3737995292690.674985403210.744813375835-0.411320879411-0.574349760503-0.450791863109-0.8841057297741.00313861274-0.0798564079043-0.0001804503155060.6018229157790.009082809647590.759739828201130.524920547-13.5638847731164.496229922
142.8211764331-0.0566312353458-1.499333664886.908908670580.5392547919420.8875504522970.540542680728-0.141341356218-0.847043700609-0.4767385245660.115383686332-0.119294254729-0.6718201062681.11811539386-0.8286667883891.595822800740.2020773711350.09949047559451.686635362260.3600229887031.08589013234143.207512768-12.5335820406133.299538263
154.940025226512.231711881771.728972916172.480660062943.51281017075.69753734423-0.848447779345-2.536426621990.5865286110910.328524204737-0.3238202605730.4877951713791.42887694768-0.115148263353-0.327036073471.706962175180.894895311156-0.1724869319892.548385921590.2686423971060.414372027137128.583353253-5.4178147986119.368185332
161.113528808741.9320296812-1.437173781293.8788287898-1.924507399411.72149268228-0.141469627342-1.814672802560.1511010860160.3611073655330.577306867157-0.1068666441310.0160768367918-0.159398618987-0.4746389601861.462833325390.308389868577-0.1625499862692.66978273078-0.4073107938551.02060084697126.150949253.37314587959124.538852744
170.9629216615140.828086233834-0.2277953128390.7649765757851.243058810375.410915019340.3092880695530.05352545094930.1188946938920.016119351948-0.8248824299220.2365980556321.076628467540.09845529090220.3087046293041.127941667330.261188131846-0.08269270574231.68195596605-0.1954535191140.812018728144124.149760144-1.6305502896124.471530672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 140 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 62 )
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 90 )
9X-RAY DIFFRACTION9chain 'B' and (resid 91 through 122 )
10X-RAY DIFFRACTION10chain 'B' and (resid 123 through 140 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 33 )
12X-RAY DIFFRACTION12chain 'C' and (resid 34 through 96 )
13X-RAY DIFFRACTION13chain 'C' and (resid 97 through 118 )
14X-RAY DIFFRACTION14chain 'D' and (resid 4 through 26 )
15X-RAY DIFFRACTION15chain 'D' and (resid 27 through 51 )
16X-RAY DIFFRACTION16chain 'D' and (resid 52 through 76 )
17X-RAY DIFFRACTION17chain 'D' and (resid 77 through 141 )

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