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- PDB-1l8q: CRYSTAL STRUCTURE OF DNA REPLICATION INITIATION FACTOR -

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Basic information

Entry
Database: PDB / ID: 1l8q
TitleCRYSTAL STRUCTURE OF DNA REPLICATION INITIATION FACTOR
ComponentsChromosomal replication initiator protein dnaA
KeywordsDNA BINDING PROTEIN / AAA+ / HELIX-TURN-HELIX / NUCLEOTIDE-BINDING / DNA BINDING / REPLICATION INITIATION
Function / homology
Function and homology information


DNA replication origin binding / regulation of DNA replication / DNA replication initiation / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Chromosomal Replication Initiator Protein Dnaa; Chain: A; / DnaA protein, C-terminal DNA-binding domain / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA ...Chromosomal Replication Initiator Protein Dnaa; Chain: A; / DnaA protein, C-terminal DNA-binding domain / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / Trp repressor/replication initiator / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsErzberger, J.P. / Pirruccello, M.M. / Berger, J.M.
CitationJournal: Embo J. / Year: 2002
Title: The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation
Authors: Erzberger, J.P. / Pirruccello, M.M. / Berger, J.M.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromosomal replication initiator protein dnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5013
Polymers38,0501
Non-polymers4522
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.752, 155.752, 155.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Chromosomal replication initiator protein dnaA


Mass: 38049.562 Da / Num. of mol.: 1 / Fragment: Residues 76-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: DNAA / Plasmid: pSV272 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: O66659
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium acetate, potassium chloride, hexanediol, PEG MME 2000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
210 mMHEPES1drop
3400 mM1dropKCl
425 mM1dropMgCl2
55 mMADP1drop
61 mMTCEP1drop
7100 mM1reservoirNaOAcpH5.0
814 %hexanediol1reservoir
915 %PEG2000 MME1reservoir
101 mMTCEP1reservoir
114 M1reservoirKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9797,1.1272
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 21, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
21.12721
ReflectionResolution: 2.7→30 Å / Num. all: 17436 / Num. obs: 17366 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 69.3 Å2 / Rsym value: 0.058 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 1720 / Rsym value: 0.33 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.415

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.034 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25484 1458 8.4 %RANDOM
Rwork0.22863 ---
all0.23083 15895 --
obs0.23083 15831 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.996 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 28 47 2713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222705
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9853621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4673319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.03915557
X-RAY DIFFRACTIONr_chiral_restr0.0940.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021961
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2780.31295
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.341
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4030.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5831.51589
X-RAY DIFFRACTIONr_mcangle_it1.17322559
X-RAY DIFFRACTIONr_scbond_it1.84731116
X-RAY DIFFRACTIONr_scangle_it3.1884.51062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 105 -
Rwork0.304 1134 -
obs-1134 98.9 %
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)
11.7356-0.9797-1.43992.62332.43854.3345-0.1206-0.023-0.1632-0.00060.0283-0.14490.08230.24140.09230.2475-0.0120.10550.23750.04270.30838.607665.459818.5388
23.70461.4827-1.87954.8248-1.60483.88530.2034-0.2433-0.13940.4236-0.21790.14190.05470.06340.01450.2978-0.13870.00640.2711-0.00930.299744.758995.876419.9505
311.4781-0.05614.88654.33631.65910.46660.7333-1.7095-0.8954-0.0199-0.40840.87940.1063-2.4509-0.3250.0151-0.0389-0.07140.65170.06540.361621.1668102.01624.3628
4-5.6979-1.7482-12.92956.03144.0968-22.02080.0877-0.10750.7053-0.8423-0.1123-0.0995-0.6193-0.3820.02460.3805-0.12890.12720.1971-0.00270.535742.369281.016119.7564
50.77740.2825-0.40362.1808-0.34940.8945-0.0218-0.1646-0.12140.04390.0035-0.2975-0.09820.08360.01830.2247-0.00650.0840.2808-0.01070.211339.080380.806915.8232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA77 - 2422 - 167
2X-RAY DIFFRACTION2AA243 - 293168 - 218
3X-RAY DIFFRACTION3AA294 - 399219 - 324
4X-RAY DIFFRACTION4AB4011
5X-RAY DIFFRACTION4AC4001
6X-RAY DIFFRACTION5AD1 - 471 - 47
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor all: 0.23083 / Rfactor obs: 0.23083 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / Rfactor Rwork: 0.304

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