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- PDB-4d8j: Structure of E. coli MatP-mats complex -

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Basic information

Entry
Database: PDB / ID: 4d8j
TitleStructure of E. coli MatP-mats complex
Components
  • 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
  • 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
  • Macrodomain Ter protein
KeywordsDNA BINDING PROTEIN / macrodomains / chromosome organization / chromosome condensation
Function / homology
Function and homology information


DNA replication termination region / chromosome organization / chromosome segregation / sequence-specific DNA binding / cell cycle / cell division / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
MatP, N-terminal domain / Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix ...MatP, N-terminal domain / Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Macrodomain Ter protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsDupaigne, P. / Tonthat, N.K. / Espeli, O. / Whitfill, T. / Boccard, F. / Schumacher, M.A.
CitationJournal: Mol.Cell / Year: 2012
Title: Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome.
Authors: Dupaigne, P. / Tonthat, N.K. / Espeli, O. / Whitfill, T. / Boccard, F. / Schumacher, M.A.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Macrodomain Ter protein
N: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
M: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
A: Macrodomain Ter protein
D: Macrodomain Ter protein
F: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
E: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
C: Macrodomain Ter protein
H: Macrodomain Ter protein
J: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
I: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
G: Macrodomain Ter protein
L: Macrodomain Ter protein
P: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
O: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
K: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)188,39816
Polymers188,39816
Non-polymers00
Water0
1
B: Macrodomain Ter protein
N: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
M: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
A: Macrodomain Ter protein

L: Macrodomain Ter protein
P: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
O: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
K: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)94,1998
Polymers94,1998
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area10740 Å2
ΔGint-68 kcal/mol
Surface area22730 Å2
2
D: Macrodomain Ter protein
F: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
E: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
C: Macrodomain Ter protein

H: Macrodomain Ter protein
J: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
I: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
G: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)94,1998
Polymers94,1998
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area23100 Å2
ΔGint-169 kcal/mol
Surface area43850 Å2
3
H: Macrodomain Ter protein
J: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
I: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
G: Macrodomain Ter protein

D: Macrodomain Ter protein
F: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
E: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
C: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)94,1998
Polymers94,1998
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area10360 Å2
ΔGint-76 kcal/mol
Surface area22820 Å2
4
L: Macrodomain Ter protein
P: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
O: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
K: Macrodomain Ter protein

B: Macrodomain Ter protein
N: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
M: 5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'
A: Macrodomain Ter protein


Theoretical massNumber of molelcules
Total (without water)94,1998
Polymers94,1998
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area22170 Å2
ΔGint-159 kcal/mol
Surface area44460 Å2
Unit cell
Length a, b, c (Å)114.870, 180.100, 184.950
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
Macrodomain Ter protein / Matp


Mass: 17725.408 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: matP, ycbG, b0956, JW0939 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8N0
#2: DNA chain
5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*TP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'


Mass: 5819.784 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: matS strand 1
#3: DNA chain
5'-D(*TP*TP*CP*GP*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*CP*GP*AP*A)-3'


Mass: 5828.798 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: mats strand 2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5% PEG 1000, 0.1 M acetate, pH 5.0, 40% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2011
RadiationMonochromator: KHOZU double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 3.55→180.1 Å / Num. all: 41400 / Num. obs: 36461 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.069 / Net I/σ(I): 7
Reflection shellResolution: 3.55→3.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.2 / % possible all: 80.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VEA

3vea


Resolution: 3.55→97.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 21487528.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.313 5473 13.2 %RANDOM
Rwork0.299 ---
obs0.299 36461 87.8 %-
all-41327 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 8.31454 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 145.4 Å2
Baniso -1Baniso -2Baniso -3
1--35.7 Å20 Å20 Å2
2---45.34 Å20 Å2
3---81.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.8 Å0.82 Å
Luzzati d res low-5 Å
Luzzati sigma a1.72 Å1.85 Å
Refinement stepCycle: LAST / Resolution: 3.55→97.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9812 3092 0 0 12904
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it3.271.5
X-RAY DIFFRACTIONc_mcangle_it5.622
X-RAY DIFFRACTIONc_scbond_it4.492
X-RAY DIFFRACTIONc_scangle_it7.182.5
LS refinement shellResolution: 3.55→3.77 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.508 937 13.4 %
Rwork0.522 6050 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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