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- PDB-3r8f: Replication initiator DnaA bound to AMPPCP and single-stranded DNA -

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Basic information

Entry
Database: PDB / ID: 3r8f
TitleReplication initiator DnaA bound to AMPPCP and single-stranded DNA
Components
  • 5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
  • Chromosomal replication initiator protein dnaA
KeywordsREPLICATION ACTIVATOR/DNA / AAA+ ATPase / Replication Initiator / DNA Binding / REPLICATION ACTIVATOR-DNA complex
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / DNA / DNA (> 10) / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.366 Å
AuthorsDuderstadt, K.E. / Chuang, K. / Berger, J.M.
CitationJournal: Nature / Year: 2011
Title: DNA stretching by bacterial initiators promotes replication origin opening.
Authors: Duderstadt, K.E. / Chuang, K. / Berger, J.M.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Feb 22, 2012Group: Non-polymer description / Refinement description
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Sep 9, 2015Group: Structure summary
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromosomal replication initiator protein dnaA
B: Chromosomal replication initiator protein dnaA
C: Chromosomal replication initiator protein dnaA
D: Chromosomal replication initiator protein dnaA
E: 5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,28013
Polymers155,1615
Non-polymers2,1188
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.797, 114.219, 201.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND NOT RESSEQ 255:265
211CHAIN A AND NOT RESSEQ 255:265
311CHAIN C AND NOT RESSEQ 255:265
411CHAIN D AND NOT RESSEQ 255:265

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Components

#1: Protein
Chromosomal replication initiator protein dnaA


Mass: 37861.984 Da / Num. of mol.: 4 / Fragment: UNP residues 76-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_322, dnaA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O66659
#2: DNA chain 5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'


Mass: 3713.524 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-35 mM sodium cacodylate, pH 6.5, 26% 1,2-propanediol, 1-2% PEG2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. all: 32862 / Num. obs: 32862 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 85.47 Å2 / Rsym value: 0.088 / Net I/σ(I): 13.5
Reflection shellResolution: 3.35→3.47 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.612 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HCB

2hcb


Resolution: 3.366→43.487 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 1663 5.07 %R-free set from PDB ENTRY 2HCB
Rwork0.249 ---
all0.2499 33228 --
obs0.2499 32803 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.672 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1804 Å20 Å2-0 Å2
2--20.585 Å2-0 Å2
3----14.4046 Å2
Refinement stepCycle: LAST / Resolution: 3.366→43.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10472 252 128 22 10874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911529
X-RAY DIFFRACTIONf_angle_d0.86414840
X-RAY DIFFRACTIONf_dihedral_angle_d18.5574397
X-RAY DIFFRACTIONf_chiral_restr0.0431648
X-RAY DIFFRACTIONf_plane_restr0.0031812
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2552X-RAY DIFFRACTIONPOSITIONAL
12A2552X-RAY DIFFRACTIONPOSITIONAL0.059
13C2552X-RAY DIFFRACTIONPOSITIONAL0.056
14D2552X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.366-3.46480.41611300.38232438X-RAY DIFFRACTION94
3.4648-3.57650.3181240.32932573X-RAY DIFFRACTION100
3.5765-3.70430.28471460.27832589X-RAY DIFFRACTION100
3.7043-3.85250.28961250.27332587X-RAY DIFFRACTION100
3.8525-4.02770.31571380.27192598X-RAY DIFFRACTION100
4.0277-4.23990.25071500.2272596X-RAY DIFFRACTION100
4.2399-4.50530.22311450.22622606X-RAY DIFFRACTION99
4.5053-4.85280.23041330.20352600X-RAY DIFFRACTION99
4.8528-5.34030.24591510.20692605X-RAY DIFFRACTION99
5.3403-6.11130.34371500.28482610X-RAY DIFFRACTION99
6.1113-7.69260.30351380.27852634X-RAY DIFFRACTION98
7.6926-43.49070.21321330.21792704X-RAY DIFFRACTION96
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)
12.13930.8747-1.01510.47220.99023.5563-0.1180.13140.06870.0426-0.17310.11480.0075-0.145-0.0010.37010.0811-0.00960.371-0.0930.3382-14.6757-16.397319.679
20.92571.39780.20351.21431.00323.9970.0711-0.07480.13330.1542-0.19340.11880.18780.080800.46410.0768-0.05090.4578-0.18610.4839-32.1692-2.124638.926
32.99891.93481.29251.07090.67691.59750.1704-0.0680.05780.1012-0.22590.0264-0.07260.047500.5288-0.0605-0.00610.4717-0.18050.5118-30.705311.864464.984
43.41860.8104-0.8330.6692-1.22022.0363-0.2894-0.0578-0.18840.0397-0.0456-0.1791-0.0063-0.138900.3624-0.05560.05010.4275-0.03460.4076-11.216926.113782.3417
50.7483-0.7457-0.26430.90020.52830.26990.1740.36-0.69170.0622-0.1903-0.0955-0.3332-0.5269-00.46610.05980.03480.7174-0.36490.6651-6.4129-35.3195-0.669
61.2756-0.655-0.13470.75320.74080.8708-0.59140.0122-0.0311-0.1745-0.05840.0070.26520.0676-0.00120.4938-0.04980.01670.6812-0.38870.6075-40.6837-20.657218.3254
70.71530.6056-0.00530.57940.1170.70560.25030.6179-0.0271-0.0205-0.61510.22410.2876-0.4439-00.6447-0.1750.17980.7024-0.46040.8355-51.1465-6.755256.5918
80.88081.18410.22631.25670.13570.63070.0253-0.16430.2782-0.6309-0.01410.46430.4594-1.157-00.6387-0.29120.00420.70670.0610.5328-31.35567.157190.835
91.77220.04370.02372.1181-2.05513.63460.6636-0.1458-0.1295-0.4947-1.1891-0.32390.49671.6215-0.26760.1196-0.0135-0.0120.0972-0.30720.6063-9.5168-57.428116.3206
101.42330.711-0.36640.7-0.57460.79860.3915-0.2321-0.4996-0.3403-0.9482-0.1713-0.6090.4811-0.0150.8161-0.16080.24660.7502-0.04360.9783-30.7741-43.05832.2968
110.03390.05560.16990.10150.1090.71810.23140.25140.30190.2215-1.02860.15540.4221-0.655-0.02191.7577-0.31420.13540.65460.01711.0636-34.1015-29.046558.9862
120.8919-0.92750.30770.2722-0.08980.01690.2032-0.25710.7898-0.2252-0.30690.32740.7809-0.2687-01.3809-0.1256-0.09340.85310.07781.0923-17.3476-14.875180.4037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 77:241A77 - 241
2X-RAY DIFFRACTION2chain B and resseq 77:241B77 - 241
3X-RAY DIFFRACTION3chain C and resseq 77:241C77 - 241
4X-RAY DIFFRACTION4chain D and resseq 77:241D77 - 241
5X-RAY DIFFRACTION5chain A and resseq 242:290A242 - 290
6X-RAY DIFFRACTION6chain B and resseq 242:290B242 - 290
7X-RAY DIFFRACTION7chain C and resseq 242:290C242 - 290
8X-RAY DIFFRACTION8chain D and resseq 242:290D242 - 290
9X-RAY DIFFRACTION9chain A and resseq 291:399A291 - 399
10X-RAY DIFFRACTION10chain B and resseq 291:399B291 - 399
11X-RAY DIFFRACTION11chain C and resseq 291:399C291 - 399
12X-RAY DIFFRACTION12chain D and resseq 291:399D291 - 399

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