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- PDB-3cwq: Crystal structure of chromosome partitioning protein (ParA) in co... -

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Basic information

Entry
Database: PDB / ID: 3cwq
TitleCrystal structure of chromosome partitioning protein (ParA) in complex with ADP from Synechocystis sp. Northeast Structural Genomics Consortium Target SgR89
ComponentsParA family chromosome partitioning protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


CobQ/CobB/MinD/ParA nucleotide binding domain / CobQ/CobB/MinD/ParA nucleotide binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ParA family chromosome partitioning protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Janjua, H. / Maglaqui, M. / Foote, E.L. / Lee, D. / Everett, J.K. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Janjua, H. / Maglaqui, M. / Foote, E.L. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of chromosome partitioning protein (ParA) in complex with ADP from Synechocystis sp.
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Janjua, H. / Maglaqui, M. / Foote, E.L. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ParA family chromosome partitioning protein
B: ParA family chromosome partitioning protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7024
Polymers45,8482
Non-polymers8542
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-2.4 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.609, 70.142, 112.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ParA family chromosome partitioning protein


Mass: 22923.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: sll6036 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6YRW8
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 Sodium chloride, 5 mM DTT. Resevoir solution: 25% Ethylene glycol, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2008 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.47→29.62 Å / Num. all: 33511 / Num. obs: 33511 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.056 / Net I/σ(I): 32.74
Reflection shellResolution: 2.47→2.54 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.96 / Rsym value: 0.155 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.47→29.62 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 25.339 / SU ML: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. Program CNS 1.2 has also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.28173 842 5.1 %RANDOM
Rwork0.22069 ---
obs0.22368 15781 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.621 Å2
Baniso -1Baniso -2Baniso -3
1--4.83 Å20 Å20 Å2
2---7.08 Å20 Å2
3---11.91 Å2
Refinement stepCycle: LAST / Resolution: 2.47→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 54 39 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0223190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6691.9934338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9695400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47224.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.58515550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9471518
X-RAY DIFFRACTIONr_chiral_restr0.1670.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2740.21533
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.22177
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.213
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.361.52080
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08923219
X-RAY DIFFRACTIONr_scbond_it3.35131306
X-RAY DIFFRACTIONr_scangle_it4.9314.51119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 48 -
Rwork0.274 788 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 74.1905 Å / Origin y: 38.4644 Å / Origin z: 65.5746 Å
111213212223313233
T-0.0214 Å20.0064 Å2-0.0135 Å2-0.0842 Å2-0.032 Å2---0.1771 Å2
L1.6093 °21.244 °2-0.4318 °2-4.6662 °2-0.7383 °2--0.5751 °2
S0.061 Å °-0.1537 Å °-0.0576 Å °0.1562 Å °-0.0591 Å °-0.1534 Å °-0.0106 Å °0.0287 Å °-0.0019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B302 - 320
2X-RAY DIFFRACTION1A302 - 322
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION1A301
5X-RAY DIFFRACTION1B1 - 201
6X-RAY DIFFRACTION1A1 - 206

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