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- PDB-3ibp: The Crystal Structure of the Dimerization Domain of Escherichia c... -

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Basic information

Entry
Database: PDB / ID: 3ibp
TitleThe Crystal Structure of the Dimerization Domain of Escherichia coli Structural Maintenance of Chromosomes Protein MukB
ComponentsChromosome partition protein mukB
KeywordsCELL CYCLE / MukB / Structural Maintenance of Chromosomes / SMC / condensin / cohesin / chromosome segregation / hinge / dimerization domain / ATP-binding / Cell division / Chromosome partition / DNA condensation / DNA-binding / Nucleotide-binding
Function / homology
Function and homology information


condensin complex / nucleoid / chromosome condensation / sister chromatid cohesion / chromosome segregation / DNA replication / cell division / GTP binding / DNA binding / ATP binding ...condensin complex / nucleoid / chromosome condensation / sister chromatid cohesion / chromosome segregation / DNA replication / cell division / GTP binding / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #850 / MukB, hinge domain / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukB, hinge domain superfamily / MukB N-terminal / MukB hinge domain / SbcC/RAD50-like, Walker B motif / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #850 / MukB, hinge domain / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukB, hinge domain superfamily / MukB N-terminal / MukB hinge domain / SbcC/RAD50-like, Walker B motif / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Chromosome partition protein MukB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.099 Å
AuthorsLi, Y. / Schoeffler, A.J. / Berger, J.M. / Oakley, M.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB.
Authors: Li, Y. / Schoeffler, A.J. / Berger, J.M. / Oakley, M.G.
History
DepositionJul 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosome partition protein mukB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6612
Polymers34,6431
Non-polymers181
Water905
1
A: Chromosome partition protein mukB
hetero molecules

A: Chromosome partition protein mukB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3214
Polymers69,2852
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_376y-2,x+2,-z+5/41
Buried area2940 Å2
ΔGint-7 kcal/mol
Surface area34720 Å2
MethodPISA
2
A: Chromosome partition protein mukB
hetero molecules

A: Chromosome partition protein mukB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3214
Polymers69,2852
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area3220 Å2
ΔGint-6 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.270, 56.270, 342.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Chromosome partition protein mukB / Structural maintenance of chromosome-related protein


Mass: 34642.629 Da / Num. of mol.: 1 / Fragment: Dimerization Domain(UNP residues 566-863)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0924, JW0907, mukB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P22523
#2: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 165 mM MOPS, 165 mM Ammonium Bromide, 13.5% PEG 20k, pH 6.5, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.971976, 0.979795, 0.979656
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9719761
20.9797951
30.9796561
ReflectionResolution: 3.099→150 Å / Num. all: 10802 / Num. obs: 10802 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 24.5
Reflection shellResolution: 3.099→3.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.5 / Num. unique all: 794 / % possible all: 83

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX2009_02_15_2320_3refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.099→56.27 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.796 / SU ML: 0.72 / σ(F): 1.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1049 10 %RANDOM
Rwork0.243 ---
obs0.247 10494 96.05 %-
all-10494 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.879 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso max: 346.33 Å2 / Biso mean: 99.631 Å2 / Biso min: 24.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.798 Å20 Å2-0 Å2
2--0.798 Å2-0 Å2
3----16.069 Å2
Refinement stepCycle: LAST / Resolution: 3.099→56.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 1 5 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082322
X-RAY DIFFRACTIONf_angle_d1.2543139
X-RAY DIFFRACTIONf_chiral_restr0.065341
X-RAY DIFFRACTIONf_plane_restr0.008429
X-RAY DIFFRACTIONf_dihedral_angle_d16.691885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.099-3.2630.3831170.3211057117478
3.263-3.4670.3571470.3231314146196
3.467-3.7350.3111510.2711357150899
3.735-4.110.2931500.2571358150899
4.11-4.7050.2521560.2111405156199
4.705-5.9260.2941560.22314031559100
5.926-56.2790.2171720.2131551172399
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.04140.4269-3.6720.2954-0.33614.3095-0.2727-0.5741-0.1514-0.1351-0.0953-0.08330.18280.93170.2740.03-0.01440.81590.00180.44144.880138.741176.558
29.3746-2.1210.96165.74191.11738.3508-0.2105-0.8644-0.16170.41890.4973-0.1207-0.35280.45330.1864-0.02830.12910.3368-0.0210.3974-52.566747.8292217.0006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain A and (resseq 572:667 or resseq 780:854)A572 - 667
2X-RAY DIFFRACTION1Chain A and (resseq 572:667 or resseq 780:854)A780 - 854
3X-RAY DIFFRACTION2Chain A and resseq 668:779A668 - 779

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