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- PDB-5hbu: Structure of the E. coli nucleoid occlusion protein SlmA bound to... -

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Basic information

Entry
Database: PDB / ID: 5hbu
TitleStructure of the E. coli nucleoid occlusion protein SlmA bound to DNA and the C-terminal tail of the cytoskeletal cell division protein FtsZ
Components
  • DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
  • FtsZ CTT peptide
  • Nucleoid occlusion factor SlmA
KeywordsCELL CYCLE/DNA / SlmA / nucleoid occlusion / FtsZ / cytokinesis / CELL CYCLE-DNA complex
Function / homology
Function and homology information


negative regulation of protein polymerization / division septum site selection / negative regulation of division septum assembly / divisome complex / bacterial nucleoid / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / sequence-specific DNA binding ...negative regulation of protein polymerization / division septum site selection / negative regulation of division septum assembly / divisome complex / bacterial nucleoid / division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / GTPase activity / regulation of DNA-templated transcription / GTP binding / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Nucleoid occlusion factor SlmA / : / Tetracyclin repressor-like, C-terminal domain / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ ...Nucleoid occlusion factor SlmA / : / Tetracyclin repressor-like, C-terminal domain / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Cell division protein FtsZ / Nucleoid occlusion factor SlmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSchumacher, M.A. / Zeng, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ.
Authors: Schumacher, M.A. / Zeng, W.
History
DepositionJan 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
C: Nucleoid occlusion factor SlmA
D: Nucleoid occlusion factor SlmA
E: Nucleoid occlusion factor SlmA
F: Nucleoid occlusion factor SlmA
G: Nucleoid occlusion factor SlmA
H: Nucleoid occlusion factor SlmA
W: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
Z: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
R: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
T: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
K: FtsZ CTT peptide


Theoretical massNumber of molelcules
Total (without water)196,96113
Polymers196,96113
Non-polymers00
Water5,459303
1
A: Nucleoid occlusion factor SlmA
B: Nucleoid occlusion factor SlmA
C: Nucleoid occlusion factor SlmA
D: Nucleoid occlusion factor SlmA
W: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
Z: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)97,8696
Polymers97,8696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-54 kcal/mol
Surface area34200 Å2
MethodPISA
2
E: Nucleoid occlusion factor SlmA
F: Nucleoid occlusion factor SlmA
G: Nucleoid occlusion factor SlmA
H: Nucleoid occlusion factor SlmA
R: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
T: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')
K: FtsZ CTT peptide


Theoretical massNumber of molelcules
Total (without water)99,0927
Polymers99,0927
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-67 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.114, 158.893, 200.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoid occlusion factor SlmA / Protein Ttk / Synthetically lethal with a defective Min system protein A


Mass: 22636.059 Da / Num. of mol.: 8 / Fragment: UNP residues 7-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: slmA, ttk, yicB, b3641, JW5641 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C093
#2: DNA chain
DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*TP*CP*AP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide FtsZ CTT peptide


Mass: 1223.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P0A9A6*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.3 M NaCl, 0.1 M TRis pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100.1 Å / Num. obs: 67564 / % possible obs: 99.5 % / Redundancy: 2 % / Rsym value: 0.124 / Net I/σ(I): 9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GCL

4gcl


Resolution: 2.6→100.1 Å / FOM work R set: 0.7687 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 2000 2.88 %
Rwork0.2262 128371 -
obs0.2275 67564 99.5 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.633 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 222.48 Å2 / Biso mean: 55.46 Å2 / Biso min: 1.79 Å2
Baniso -1Baniso -2Baniso -3
1--8.134 Å20 Å2-0 Å2
2--23.4457 Å20 Å2
3----15.3117 Å2
Refinement stepCycle: final / Resolution: 2.6→100.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12435 972 0 303 13710
Biso mean---40.59 -
Num. residues----1580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313684
X-RAY DIFFRACTIONf_angle_d0.5918596
X-RAY DIFFRACTIONf_chiral_restr0.0382115
X-RAY DIFFRACTIONf_plane_restr0.0022248
X-RAY DIFFRACTIONf_dihedral_angle_d17.5925370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.69290.38743850.319127651315099
2.6929-2.80080.36563790.30381288213261100
2.8008-2.92820.38743840.29651283413218100
2.9282-3.08260.35153830.27081285113234100
3.0826-3.27580.27943750.24751287613251100
3.2758-3.52870.28393820.22631289013272100
3.5287-3.88380.26663740.21531288613260100
3.8838-4.44580.23153850.18081281613201100
4.4458-5.60120.21323750.1835128321320799
5.6012-100.17470.20723870.2046127391312699
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)
1-0.01010.0074-0.0358-0.0166-0.00750.0087-0.00460.0757-0.2235-0.04660.4150.3852-0.20810.2731-0-0.1360.1760.70510.5654-0.4031-1.31129.3401-34.309267.3068
20.00160.0019-0.01260.00410.0011-00.2204-0.06550.2337-0.0380.42930.17960.11050.2880-0.34220.7341-0.1441-0.4147-0.06270.06436.1606-44.409583.2595
3-0.0401-0.0695-0.0359-0.02220.02030.00850.0014-0.4059-0.80060.2039-0.1423-0.10460.2924-0.113200.261.0470.1456-0.7249-0.7088-0.17133.9139-57.653887.2041
4-0.00130.0160.00240.01330.01670.01480.2744-0.15960.2840.0790.07140.13460.11950.1112-00.29570.0884-0.02730.15380.00810.1229-2.5128-42.173190.6947
50-0.002-0.0012-0.0030.0014-0.0008-0.0069-0.0060.0006-0.03520.01960.04460.0041-0.011100.9541-0.01060.11751.2883-0.00661.087-36.581-38.306763.9527
60.00730.00940.0174-0.0039-0.01220.02260.08220.03280.0566-0.15580.051-0.14810.0436-0.10600.36290.03620.02741.1248-0.09490.2812-22.4635-39.125365.9723
70.0606-0.04450.002-0.0277-0.04380.00340.1585-0.0194-0.0086-0.0863-0.38080.03160.0354-0.380400.3137-0.09890.04430.3123-0.06210.2335-19.6016-41.498588.1655
80.0297-0.00440.0096-0.00080.00880.00430.1045-0.2178-0.0873-0.02130.02630.01150.1043-0.0401-00.452-0.02510.00620.16720.01780.3029-10.7417-48.880390.3298
90.0347-0.0027-0.0165-0.01110.01520.01890.0307-0.1542-0.6959-0.05060.1044-0.082-0.132-0.284900.1670.04320.09030.2317-0.0551-0.2274-9.7278-34.392733.9581
100.0418-0.0533-0.029-0.0077-0.00140.0233-0.1183-0.09740.0765-0.01810.00740.1239-0.0427-0.038-00.05090.0256-0.0180.046-0.020.0838-5.5566-45.673118.3
11-0.01420.00220.015-0.00310.0101-0.0045-0.22780.0554-0.18740.1829-0.02980.0015-0.04380.018800.0617-0.1848-0.0228-0.6581-0.08510.1214-5.4152-60.35039.3255
120.047-0.01540.02530.0164-0.0093-0.02770.0262-0.0753-0.0101-0.11670.023-0.04150.3058-0.1644-0-0.46040.4244-0.0081-0.36940.00980.13493.0613-45.19249.0046
13-0.0022-0.02080.02960.023-0.00070.0004-0.0255-0.1064-0.05460.0722-0.06210.25190.05130.189200.2323-0.0465-0.02760.8594-0.11130.089322.7193-37.120537.996
140.02120.0534-0.0206-0.01960.01610.020.0195-0.4662-0.207-0.2075-0.13930.0273-0.19780.40320-0.0269-0.0293-0.0366-0.0584-0.04810.070420.6319-39.96816.8772
15-0.0034-0.0029-0.0051-0.01870.0056-0.0012-0.03940.04060.09380.2550.02830.2204-0.1219-0.04520-0.4611-0.27560.0715-0.0650.04060.031820.8258-39.4278-3.6619
160.0534-0.0153-0.0088-0.00950.0306-0.0055-0.01330.0525-0.0344-0.17380.04080.1507-0.19490.09160-1.3246-0.5445-0.0021-0.44210.02390.083211.6383-48.477110.52
170.0013-0.0033-0.0012-0.00130.0002-0.00040.0168-0.0055-0.01970.01480.0028-0.05090.02120.025200.6051-0.1481-0.03680.62550.02050.657917.74276.338950.0523
18-0.00940.005-0.0135-0.0028-0.0010.0016-0.15970.02110.04160.02140.03930.008-0.14320.0248-00.2851-0.01120.03010.0979-0.06280.21196.75078.659246.5759
190.06810.05770.0885-0.0143-0.04810.05590.0452-0.1716-0.0253-0.0559-0.00220.0835-0.01660.2596-00.16430.0492-0.01680.1735-0.08240.18323.6418-7.665966.6011
200.01210.0012-0.0052-0.0004-0.00120.00990.1160.0290.10310.04880.02620.02130.0695-0.032600.18940.00120.02590.4684-0.12130.1988-1.705-2.088679.1042
210.00660.02040.00540.0077-0.01670.0053-0.05070.0701-0.1672-0.03540.112-0.12810.0947-0.2281-00.1750.010.00750.61160.04760.094-22.93461.762245.2958
220.01620.0037-0.0306-0.0049-0.00240.00470.05360.023-0.1407-0.0238-0.0471-0.10550.0024-0.173100.18530.02970.00430.2078-0.08210.1606-24.6119-4.345370.4291
230.0242-0.0393-0.0265-0.0387-0.0407-0.0018-0.2348-0.15980.0208-0.2254-0.10640.0886-0.1040.0064-00.22430.05640.01750.1968-0.08220.2087-17.32564.328569.8567
240.032-0.0096-0.01230.0093-0.01890.00590.0642-0.1908-0.2640.0417-0.1808-0.0191-0.1058-0.024200.05550.06210.0348-0.0439-0.15510.0281-11.6618-7.952272.6342
250.00610.00150.01170.00770.01720.0090.032-0.0020.01010.05730.123-0.1183-0.1812-0.1098-00.2720.05360.02240.46210.03410.2255-9.27177.029917.5284
260.07280.027-0.0448-0.09610.10570.0314-0.01140.0514-0.010.1258-0.02160.13690.04930.006900.0137-0.08830.0322-0.09170.11330.0492-5.9265-7.99372.5912
27-0.00130.01630.0227-0.00050.012-0.0091-0.0341-0.0006-0.13370.09990.144-0.0907-0.07030.02600.1649-0.0208-0.01440.17140.040.26950.7308-15.5063-7.9797
280.0088-0.0023-0.00430.008-0.01420.0017-0.00480.1024-0.08490.1693-0.0449-0.0078-0.2655-0.0138-00.2036-0.0076-0.0240.27790.06560.20452.0156-2.7835-11.5125
290.00870.00840.01560.01890.00390.0066-0.0405-0.09760.04630.0210.06460.10560.1950.210300.158-0.00660.01180.1844-0.05110.157923.53211.311618.2589
300.0375-0.00270.001-0.0101-0.01010.02670.06080.08480.02320.0291-0.0871-0.0468-0.03680.3002-00.1075-0.0177-0.00150.01150.07390.255920.2373-2.4122-1.5209
310.001-0.0035-0.00440.0005-0.00250.0029-0.15460.03710.01810.1226-0.01250.0155-0.06460.00300.1874-0.0735-0.01250.4070.08150.232520.806-1.1235-21.0819
320.0436-0.00840.00920.02290.03190.00850.02580.1098-0.12990.079-0.07270.0439-0.18760.0361-00.05860.0025-0.00960.10480.03720.183811.6579-10.2144-6.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 9:73)A9 - 73
2X-RAY DIFFRACTION2(chain A and resid 74:120)A74 - 120
3X-RAY DIFFRACTION3(chain A and resid 121:157)A121 - 157
4X-RAY DIFFRACTION4(chain A and resid 158:198)A158 - 198
5X-RAY DIFFRACTION5(chain B and resid 3:14)B3 - 14
6X-RAY DIFFRACTION6(chain B and resid 15:72)B15 - 72
7X-RAY DIFFRACTION7(chain B and resid 73:148)B73 - 148
8X-RAY DIFFRACTION8(chain B and resid 149:198)B149 - 198
9X-RAY DIFFRACTION9(chain C and resid 9:68)C9 - 68
10X-RAY DIFFRACTION10(chain C and resid 69:129)C69 - 129
11X-RAY DIFFRACTION11(chain C and resid 130:149)C130 - 149
12X-RAY DIFFRACTION12(chain C and resid 150:198)C150 - 198
13X-RAY DIFFRACTION13(chain D and resid 10:59)D10 - 59
14X-RAY DIFFRACTION14(chain D and resid 60:134)D60 - 134
15X-RAY DIFFRACTION15(chain D and resid 135:149)D135 - 149
16X-RAY DIFFRACTION16(chain D and resid 150:198)D150 - 198
17X-RAY DIFFRACTION17(chain E and resid 9:17)E9 - 17
18X-RAY DIFFRACTION18(chain E and resid 18:56)E18 - 56
19X-RAY DIFFRACTION19(chain E and resid 57:179)E57 - 179
20X-RAY DIFFRACTION20(chain E and resid 180:198)E180 - 198
21X-RAY DIFFRACTION21(chain F and resid 10:63)F10 - 63
22X-RAY DIFFRACTION22(chain F and resid 64:106)F64 - 106
23X-RAY DIFFRACTION23(chain F and resid 107:149)F107 - 149
24X-RAY DIFFRACTION24(chain F and resid 150:198)F150 - 198
25X-RAY DIFFRACTION25(chain G and resid 9:56)G9 - 56
26X-RAY DIFFRACTION26(chain G and resid 57:137)G57 - 137
27X-RAY DIFFRACTION27(chain G and resid 138:176)G138 - 176
28X-RAY DIFFRACTION28(chain G and resid 177:198)G177 - 198
29X-RAY DIFFRACTION29(chain H and resid 9:68)H9 - 68
30X-RAY DIFFRACTION30(chain H and resid 69:134)H69 - 134
31X-RAY DIFFRACTION31(chain H and resid 135:149)H135 - 149
32X-RAY DIFFRACTION32(chain H and resid 150:198)H150 - 198

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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