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- PDB-3sk7: Crystal Structure of V. cholerae SeqA -

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Basic information

Entry
Database: PDB / ID: 3sk7
TitleCrystal Structure of V. cholerae SeqA
ComponentsProtein SeqA
KeywordsREPLICATION INHIBITOR / Sequestration / Negative regulator / DNA replication initiation / DNA binding
Function / homologyReplication modulator SeqA, C-terminal DNA-binding domain / Replication modulator SeqA, C-terminal DNA-binding domain / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChung, Y.S. / Guarne, A.
CitationJournal: To be Published
Title: Investigating the aggregational property of SeqAvibrio in the absence of the oligomerization domain
Authors: Chung, Y.S. / Guarne, A.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Atomic model
Revision 1.2Sep 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SeqA
B: Protein SeqA


Theoretical massNumber of molelcules
Total (without water)26,5712
Polymers26,5712
Non-polymers00
Water4,288238
1
A: Protein SeqA


Theoretical massNumber of molelcules
Total (without water)13,2851
Polymers13,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein SeqA


Theoretical massNumber of molelcules
Total (without water)13,2851
Polymers13,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.008, 55.029, 135.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT NO QUATERNARY STRUCTURES WERE DETECTED.

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Components

#1: Protein Protein SeqA


Mass: 13285.413 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: A5C_2175, seqA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A3GNC8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDApr 30, 2010Mirrors
ADSC QUANTUM 3152CCDNov 9, 2010Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.11
ReflectionResolution: 1.46→50 Å / Num. obs: 35671 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.266
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4.403 / Rsym value: 0.462 / % possible all: 98.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3FMT

3fmt


Resolution: 1.5→34.918 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.81 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 1797 5.04 %Random
Rwork0.1564 ---
obs0.1587 35671 99.57 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.972 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8822 Å20 Å2-0 Å2
2--3.0873 Å2-0 Å2
3----2.205 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 238 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011914
X-RAY DIFFRACTIONf_angle_d1.0682598
X-RAY DIFFRACTIONf_dihedral_angle_d17.743745
X-RAY DIFFRACTIONf_chiral_restr0.066302
X-RAY DIFFRACTIONf_plane_restr0.006335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54060.21551220.15112604X-RAY DIFFRACTION99
1.5406-1.58590.21271460.15232526X-RAY DIFFRACTION99
1.5859-1.63710.19431360.14232558X-RAY DIFFRACTION99
1.6371-1.69560.20671220.13782579X-RAY DIFFRACTION100
1.6956-1.76350.1921330.13852539X-RAY DIFFRACTION100
1.7635-1.84370.20781320.13962607X-RAY DIFFRACTION100
1.8437-1.94090.19411660.14442588X-RAY DIFFRACTION100
1.9409-2.06250.2051520.14652570X-RAY DIFFRACTION100
2.0625-2.22170.18841530.14642596X-RAY DIFFRACTION100
2.2217-2.44530.17231450.14272585X-RAY DIFFRACTION100
2.4453-2.7990.22591260.15282648X-RAY DIFFRACTION100
2.799-3.52590.21611310.16872687X-RAY DIFFRACTION100
3.5259-34.92730.21131330.17852787X-RAY DIFFRACTION98

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