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- PDB-3anw: A protein complex essential initiation of DNA replication -

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Basic information

Entry
Database: PDB / ID: 3anw
TitleA protein complex essential initiation of DNA replication
Components(Putative uncharacterized protein) x 2
KeywordsREPLICATION / sld5 superfamily / DNA replication
Function / homology
Function and homology information


Archaeal GINS complex, Gins51 subunit / : / Gins51, C-terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2050 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Ribosomal Protein L9; domain 1 - #50 / Ribosomal Protein L9; domain 1 / GINS complex, subunit Psf3 superfamily / GINS subunit, domain A / GINS complex protein helical bundle domain ...Archaeal GINS complex, Gins51 subunit / : / Gins51, C-terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2050 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Ribosomal Protein L9; domain 1 - #50 / Ribosomal Protein L9; domain 1 / GINS complex, subunit Psf3 superfamily / GINS subunit, domain A / GINS complex protein helical bundle domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Gins51 C-terminal domain-containing protein / GINS subunit domain-containing protein
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.65 Å
AuthorsOyama, T. / Shirai, T. / Nagasawa, N. / Ishino, Y. / Morikawa, K.
CitationJournal: Bmc Biol. / Year: 2011
Title: Architectures of archaeal GINS complexes, essential DNA replication initiation factors
Authors: Oyama, T. / Ishino, S. / Fujino, S. / Ogino, H. / Shirai, T. / Mayanagi, K. / Saito, M. / Nagasawa, N. / Ishino, Y. / Morikawa, K.
History
DepositionSep 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,6532
Polymers41,6532
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.343, 76.343, 181.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative uncharacterized protein / gins51


Mass: 21623.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0536 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5JF31
#2: Protein Putative uncharacterized protein / gins23


Mass: 20029.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK1619 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5JIT2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.2M magnesium chloride, 24% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 5, 2010
RadiationMonochromator: FIXED EXIT SI 111 DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→37.35 Å / Num. all: 16278 / Num. obs: 16278 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.6
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 14 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1598 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.65→37.35 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 116289.88 / 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
Rfree0.31 754 4.8 %RANDOM
Rwork0.262 ---
obs0.262 15628 95.7 %-
all-16382 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9503 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 64.8 Å2
Baniso -1Baniso -2Baniso -3
1-15.38 Å20 Å20 Å2
2--15.38 Å20 Å2
3----30.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.65→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 0 33 2655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.672.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.461 105 4.4 %
Rwork0.37 2272 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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