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- PDB-2z4r: Crystal structure of domain III from the Thermotoga maritima repl... -

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Basic information

Entry
Database: PDB / ID: 2z4r
TitleCrystal structure of domain III from the Thermotoga maritima replication initiation protein DnaA
ComponentsChromosomal replication initiator protein dnaA
KeywordsDNA BINDING PROTEIN / AAA+ ATPase / domain III (ATPase domain) / ATP-binding / Cytoplasm / DNA replication / DNA-binding / Nucleotide-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DNA replication origin binding / regulation of DNA replication / DNA replication initiation / DNA replication / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / 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 ...DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsFujikawa, N. / Ozaki, S. / Kagawa, W. / Park, S.-Y. / Katayama, T. / Kurumizaka, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A Common Mechanism for the ATP-DnaA-dependent Formation of Open Complexes at the Replication Origin
Authors: Ozaki, S. / Kawakami, H. / Nakamura, K. / Fujikawa, N. / Kagawa, W. / Park, S.-Y. / Yokoyama, S. / Kurumizaka, H. / Katayama, T.
History
DepositionJun 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4989
Polymers151,1443
Non-polymers1,3556
Water724
1
A: Chromosomal replication initiator protein dnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8333
Polymers50,3811
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chromosomal replication initiator protein dnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8333
Polymers50,3811
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chromosomal replication initiator protein dnaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8333
Polymers50,3811
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.335, 221.787, 55.601
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Chromosomal replication initiator protein dnaA


Mass: 50381.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: dnaA / Plasmid: pBAD18 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P46798
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 3 / 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.: 4 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M LITHIUM SULFATE, 0.05M MAGNESIUM SULFATE, 0.05M Na-HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2004 / Details: monochromator
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 29524 / Num. obs: 27762 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2015 / % possible all: 68.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L8Q

1l8q


Resolution: 3.05→48.12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2761 -random
Rwork0.231 ---
all0.264 29468 --
obs0.232 27730 94.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.05→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5817 0 84 4 5905
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00777
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
3.05-3.240.43860.362X-RAY DIFFRACTION32336
3.24-3.490.2914500.272X-RAY DIFFRACTION41686
3.49-3.840.2594480.218X-RAY DIFFRACTION43296
3.84-4.40.2535210.208X-RAY DIFFRACTION43786
4.4-5.540.2194770.191X-RAY DIFFRACTION44136
5.54-500.2724790.246X-RAY DIFFRACTION44486

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