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- PDB-5k5z: Structure of pnob8 ParA -

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Basic information

Entry
Database: PDB / ID: 5k5z
TitleStructure of pnob8 ParA
ComponentsParA
KeywordsHYDROLASE / partition / segregation / pnob8
Function / homology: / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AAA domain-containing protein
Function and homology information
Biological speciesSulfolobus sp. NOB8H2 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.369 Å
AuthorsSchumacher, M.
CitationJournal: Science / Year: 2015
Title: Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Authors: Schumacher, M.A. / Tonthat, N.K. / Lee, J. / Rodriguez-Castaneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJun 22, 2016ID: 4RU8
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ParA
B: ParA
C: ParA
D: ParA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2258
Polymers145,1644
Non-polymers1,0614
Water4,756264
1
A: ParA
D: ParA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6436
Polymers72,5822
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-51 kcal/mol
Surface area22900 Å2
MethodPISA
2
B: ParA
C: ParA


Theoretical massNumber of molelcules
Total (without water)72,5822
Polymers72,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-24 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.700, 305.600, 84.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
ParA


Mass: 36291.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus sp. NOB8H2 (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: O93708
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 8000, 20% PEG 400, 100 mM Magnesium chloride, 100 mM Tris pH 8.5

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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 315r / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.369→76.4 Å / Num. obs: 45617 / % possible obs: 83.86 % / Redundancy: 2 % / Rsym value: 0.043 / Net I/σ(I): 17

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.369→76.4 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 1999 4.38 %
Rwork0.2074 43618 -
obs0.2099 45617 83.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 102.03 Å2 / Biso mean: 43.3569 Å2 / Biso min: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1-13.0791 Å2-0 Å2-0 Å2
2---8.9057 Å20 Å2
3----9.012 Å2
Refinement stepCycle: final / Resolution: 2.369→76.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9887 0 64 264 10215
Biso mean--40.09 39.09 -
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410206
X-RAY DIFFRACTIONf_angle_d1.0413798
X-RAY DIFFRACTIONf_chiral_restr0.0951541
X-RAY DIFFRACTIONf_plane_restr0.0041739
X-RAY DIFFRACTIONf_dihedral_angle_d17.9043937
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 (%)
2.3693-2.4540.3211920.25732023211539
2.454-2.55230.361250.25142710283553
2.5523-2.66840.33431600.24433495365568
2.6684-2.80910.2941960.24264280447683
2.8091-2.98510.30952280.23754969519796
2.9851-3.21560.30372360.242651395375100
3.2156-3.53920.28052370.223251885425100
3.5392-4.05130.25292380.19065194543299
4.0513-5.10410.21072400.164552215461100
5.1041-76.43970.23832470.2015399564699

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