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- PDB-8dss: X-ray crystal structure of Geobacillus stearothermophilus ComEA -

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Basic information

Entry
Database: PDB / ID: 8dss
TitleX-ray crystal structure of Geobacillus stearothermophilus ComEA
ComponentsComE operon protein 1
KeywordsDNA BINDING PROTEIN / plasma membrane / DNA binding / genetic competence / oligomerization
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / DNA repair / DNA binding / membrane
Similarity search - Function
Competence protein ComEA, helix-hairpin-helix domain / : / Helix-hairpin-helix motif / Soluble ligand binding domain / SLBB domain / RuvA domain 2-like / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1
Similarity search - Domain/homology
ComEA family DNA-binding protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus ATCC 7953 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsAhmed, I. / Neiditch, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM057720 United States
Citation
Journal: Nat Commun / Year: 2022
Title: Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria.
Authors: Ahmed, I. / Hahn, J. / Henrickson, A. / Khaja, F.T. / Demeler, B. / Dubnau, D. / Neiditch, M.B.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJul 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: ComE operon protein 1
B: ComE operon protein 1


Theoretical massNumber of molelcules
Total (without water)31,3132
Polymers31,3132
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.706, 80.706, 71.279
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein ComE operon protein 1 / ComEA family DNA-binding protein / Late competence protein ComEA DNA receptor


Mass: 15656.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus ATCC 7953 (bacteria)
Gene: B4109_2104, B4114_2221, D9548_03605, GS458_2294, TGS27_0901
Plasmid: pTB146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K9HI54
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 400, 0.1M ammonium nitrate

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 5194 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 51.71 Å2 / CC1/2: 0.929 / Net I/σ(I): 9.38
Reflection shellResolution: 3.05→3.1 Å / Num. unique obs: 273 / CC1/2: 0.429

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DFK

8dfk


Resolution: 3.05→40.35 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 515 10.14 %
Rwork0.2262 4562 -
obs0.2319 5077 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.55 Å2
Refinement stepCycle: LAST / Resolution: 3.05→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 0 2 1424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331438
X-RAY DIFFRACTIONf_angle_d0.481947
X-RAY DIFFRACTIONf_chiral_restr0.0455232
X-RAY DIFFRACTIONf_plane_restr0.0042255
X-RAY DIFFRACTIONf_dihedral_angle_d6.3649202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.360.38861290.29581144X-RAY DIFFRACTION99.61
3.36-3.840.27021290.23911135X-RAY DIFFRACTION99.84
3.84-4.840.25941250.19911133X-RAY DIFFRACTION99.6
4.84-40.350.27131320.21161150X-RAY DIFFRACTION98.62
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)
18.10662467653-1.81117053258-4.202145540054.80266347152-1.574305401557.52736814159-0.1094171878990.2749957095140.680540891956-0.150711494703-0.316849037174-0.7283756864150.9038376012661.4385022765-0.4863959751020.4605864849360.023302357868-0.1033522858560.258995128031-0.07947572960920.27753305913121.343442500934.262771490520.324878678
28.74679924636-5.67757132726-0.3163756382515.16230933898-0.5153229659822.729253501390.555242527222-1.044802185020.03615145694430.5756998754110.541640738162-0.31540602875-0.775938913011-0.15255854151-0.6753474223940.4278165152740.158922434506-0.03818875901370.515538714845-0.08588198658620.35891589966617.664421719337.419848900325.9445002982
35.93277843361.415197867253.082663120388.366542566433.821072991923.393505014720.2040770971730.6556943143240.12859625703-0.2815251594880.094648333283-0.60836090570.4271291405070.865990951474-0.3344792583410.2275790572250.04062560706720.03255516141460.3465017178750.07776985788580.22842444302114.79264643137.127614454912.4103933646
49.26910623652-5.816591407096.184306205333.6855103463-3.965350722477.62299832801-0.525229110455-0.767595351146-0.1916633669920.2305389361290.6080501084990.2758067555230.209275979418-1.081597451850.01618631373630.365702625061-0.08342164901160.007769234239350.275511346512-0.06721116664210.32939567430712.036235390932.238354127723.489473163
52.469012539970.4023138641842.845137153065.62702316839-2.781834806358.405682824480.5487830459750.859940465965-0.40700668065-0.281032537578-0.768375013639-1.115524625041.13785822439-0.154875629038-0.02482830023950.4477346841360.1147687901440.02275170132740.645144089052-0.06701884562510.60836747064716.535997783828.449699680211.6017921444
62.800382411881.075162998160.5549321040413.84820194022-0.6632608266415.202799652840.0690393086782-0.34549533563-0.03280531948510.1327636537490.06516353234820.3005361796720.18867026053-0.131360715091-0.1481942400980.216522546130.01766489579290.02728674249960.227110603165-0.01132178582430.201167130671-2.8826086901339.442090001613.3669454853
76.72460377181-0.787118241209-5.213556023410.6056953538840.6493915306424.25701734274-0.4192338098381.000407525680.4665887462040.2865451262490.344230604742-0.3031437463170.553131165544-0.2853704349540.9345189830010.5452951854560.04408993286010.0361119241430.5950798749010.04033230130360.6873727111344.5725290361231.4630174306-8.95906495506
87.070042453030.60323563714-3.535546136934.80193128242-5.564092958247.79778042671-0.3936892884820.0622132261595-1.20704913275-1.107979368690.8980279865490.7127051167061.441354005470.0227684362495-0.4019139260420.769544847137-0.0473264865166-0.04527771901130.578535475298-0.2557864397441.204275211895.572689437424.0386303424-21.5834182977
96.4104647984-1.416507679724.953033091678.246241627522.847239901698.197456847390.4246754178260.543417679685-0.720153726441-0.938518019999-0.4342000067361.34788684566-0.2081309659090.09308376264550.06522976737710.585737667165-0.0450044525053-0.07380762693620.44320023758-0.09570196050140.602563302343-1.6722937618432.9266050639-23.5679069458
100.3020607745290.721673259125-0.2170470401562.759106965881.009700913422.37272924163-0.987399815325-0.12886171787-0.3434095114750.756865930245-0.1118440997391.664947660260.470872996435-0.6503877461850.408433413320.431047140349-0.08124646325070.04790482206490.4357597750760.004005640227791.03190625494-0.053592445178632.8199281931-13.7544789002
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 62 through 75 )AA62 - 751 - 14
22chain 'A' and (resid 76 through 85 )AA76 - 8515 - 24
33chain 'A' and (resid 86 through 104 )AA86 - 10425 - 43
44chain 'A' and (resid 105 through 114 )AA105 - 11444 - 53
55chain 'A' and (resid 115 through 124 )AA115 - 12454 - 63
66chain 'B' and (resid 62 through 119 )BB62 - 1191 - 58
77chain 'B' and (resid 120 through 152 )BB120 - 15259 - 73
88chain 'B' and (resid 153 through 176 )BB153 - 17674 - 97
99chain 'B' and (resid 177 through 199 )BB177 - 19998 - 120
1010chain 'B' and (resid 200 through 207 )BB200 - 207121 - 128

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