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- PDB-5u1j: Structure of pNOB8 ParA bound to nonspecific DNA -

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Basic information

Entry
Database: PDB / ID: 5u1j
TitleStructure of pNOB8 ParA bound to nonspecific DNA
Components
  • DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)-3')
  • Uncharacterized protein
KeywordsDNA BINDING PROTEIN/DNA / ParA / nonspecific DNA binding / nucleoid / segregation / ParB / DNA BINDING PROTEIN-DNA complex
Function / homologyAAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / AAA domain-containing protein
Function and homology information
Biological speciesSulfolobus sp. NOB8H2 (acidophilic)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsSchumacher, M.A.
CitationJournal: Genes Dev. / Year: 2017
Title: Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation.
Authors: Zhang, H. / Schumacher, M.A.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Uncharacterized protein
A: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
U: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)-3')
W: DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,98510
Polymers160,9606
Non-polymers2,0254
Water00
1
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0364
Polymers74,0242
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-31 kcal/mol
Surface area22580 Å2
MethodPISA
2
A: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0364
Polymers74,0242
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-29 kcal/mol
Surface area22460 Å2
MethodPISA
3
U: DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)-3')
W: DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,9132
Polymers12,9132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-5 kcal/mol
Surface area7940 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-75 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 103.700, 104.000
Angle α, β, γ (deg.)90.000, 101.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 37011.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus sp. NOB8H2 (acidophilic) / Plasmid: pNOB8 / Production host: Escherichia coli (E. coli) / References: UniProt: O93708
#2: DNA chain DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)-3')


Mass: 6449.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3')


Mass: 6464.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 4000, 10% isopropanol, 0.1 M Citrate pH 5.5

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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 210r / Detector: CCD / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→103.66 Å / Biso Wilson estimate: 73.76 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.05 / Rsym value: 0.073
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4260 / CC1/2: 0.797 / Rpim(I) all: 0.416 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5Z

5k5z


Resolution: 2.95→53.098 Å / FOM work R set: 0.7889 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1997 6.9 %
Rwork0.2204 26945 -
obs0.2223 28942 96.26 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.01 Å2 / ksol: 0.266 e/Å3
Displacement parametersBiso max: 314.16 Å2 / Biso mean: 98.83 Å2 / Biso min: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1--25.0585 Å20 Å26.4554 Å2
2--25.9665 Å2-0 Å2
3----0.9079 Å2
Refinement stepCycle: final / Resolution: 2.95→53.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9375 857 35 0 10267
Biso mean--168.17 --
Num. residues----1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710667
X-RAY DIFFRACTIONf_angle_d0.94414600
X-RAY DIFFRACTIONf_chiral_restr0.4271640
X-RAY DIFFRACTIONf_plane_restr0.0021682
X-RAY DIFFRACTIONf_dihedral_angle_d20.0774206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9499-3.05540.37722010.33832691289297
3.0554-3.17770.37291970.30372684288197
3.1777-3.32230.312010.27852707290897
3.3223-3.49740.34162000.26632710291097
3.4974-3.71650.27442010.25662697289897
3.7165-4.00330.25822010.222718291997
4.0033-4.4060.23041990.19062672287196
4.406-5.04320.19312010.17112712291396
5.0432-6.35220.22161990.21472684288395
6.3522-53.10620.21771970.20022670286793
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)
12.1227-0.2638-0.5739-0.0854-0.27511.1866-0.17440.1913-0.3675-0.02890.05150.00230.0931-0.03910.16190.3868-0.05930.04190.2229-0.02670.25950.543112.725934.9535
21.3707-0.1654-0.69261.17160.12270.83710.1019-0.07360.17790.21870.17850.13710.0337-0.0151-0.20730.2728-0.02420.03030.1802-0.01650.1737-7.962226.499246.0951
30.70920.77450.2911.3767-0.38680.660.1535-0.2667-0.5465-0.0003-0.1434-0.17840.4504-0.1416-0.04760.68160.00550.07280.45860.13460.5841-2.15747.841549.9306
42.0691-0.665-0.31511.05850.14050.01010.1815-0.1453-0.02640.0866-0.35140.10530.0931-0.13290.09360.266-0.1410.00410.3229-0.15410.1907-12.1094-1.3034-5.2488
50.83560.3056-0.74490.62810.12670.71110.05220.12940.6226-0.0858-0.13841.0224-0.2038-0.0241-0.15830.330.0920.02250.363-0.06750.978-15.180219.7993-11.7671
60.59180.406-0.32170.77080.10620.41530.5354-0.41060.15210.1326-0.59290.3818-0.1098-0.16880.18780.3001-0.14710.07180.7748-0.46380.562-11.371211.62416.1707
71.2093-0.5426-0.09820.52820.68641.46950.08471.52620.12850.75630.5688-0.32720.37210.2859-0.1168-0.0175-0.48990.2132-1.24340.48590.215812.096710.0679-19.7431
81.8834-0.09890.58981.55571.05060.8120.2290.244-0.09640.07840.061-0.23150.1750.1089-0.18230.31970.0002-0.00050.31940.01870.238413.5922-5.396-16.4724
91.60951.1481-0.01281.09220.03751.33310.3133-0.32240.5460.0924-0.022-0.1076-0.15130.5893-0.23510.168-0.092-0.00970.3603-0.11350.274820.52185.3755-2.8565
103.0014-0.4949-0.53660.3298-0.23290.29380.12650.19820.5176-0.0728-0.2034-0.2568-0.06660.1390.1120.4002-0.0588-0.03460.50390.1170.562321.44532.072540.095
110.62480.48980.10281.1305-0.02540.98720.15070.0199-0.5333-0.0951-0.9212-0.62410.36590.57480.65330.47380.11810.06180.58690.1430.899528.82211.986337.4528
120.70410.3829-0.11521.1473-0.45571.08620.0829-0.8486-0.06080.2659-0.2171-0.6827-0.15890.05670.24060.5697-0.1033-0.17910.83380.24710.732128.355923.307252.4882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:113)A2 - 115
2X-RAY DIFFRACTION2(chain A and resid 118:254)A116 - 254
3X-RAY DIFFRACTION3(chain A and resid 255:315)A255 - 315
4X-RAY DIFFRACTION4(chain B and resid 2:206)B2 - 206
5X-RAY DIFFRACTION5(chain B and resid 207:262)B207 - 262
6X-RAY DIFFRACTION6(chain B and resid 263:315)B263 - 315
7X-RAY DIFFRACTION7(chain C and resid 2:103)C2 - 103
8X-RAY DIFFRACTION8(chain C and resid 104:206)C104 - 206
9X-RAY DIFFRACTION9(chain C and resid 207:315)C207 - 315
10X-RAY DIFFRACTION10(chain D and resid 2:206)D2 - 206
11X-RAY DIFFRACTION11(chain D and resid 207:262)D207 - 262
12X-RAY DIFFRACTION12(chain D and resid 263:315)D263 - 315

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