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- PDB-1u99: Crystal Structures of E. coli RecA in a Compressed Helical Filame... -

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Basic information

Entry
Database: PDB / ID: 1u99
TitleCrystal Structures of E. coli RecA in a Compressed Helical Filament Form 4
ComponentsRecA protein
KeywordsDNA BINDING PROTEIN / RecA / hoomologous recombination / ATPase / DNA repair
Function / homology
Function and homology information


DNA polymerase V complex / homologous recombination / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein ...RecA protein, C-terminal domain / Rec A Protein; domain 2 / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein RecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXing, X. / Bell, C.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of Escherichia coli RecA in a compressed helical filament.
Authors: Xing, X. / Bell, C.E.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 5, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: RecA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3942
Polymers38,2991
Non-polymers951
Water61334
1
A: RecA protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)230,36112
Polymers229,7916
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
crystal symmetry operation3_555-x+y,-x,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+5/61
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)108.001, 108.001, 74.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological assembly is a continuous helical filament generated by the 6sub1 symmetry operators

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Components

#1: Protein RecA protein / / Recombinase A


Mass: 38298.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RecA with N-terminal GSHM residues / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recA / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P0A7G6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 200, sodium citrate, sodium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: SBC-2 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→31.18 Å / Num. all: 15111 / Num. obs: 14222 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 47.9 Å2 / Limit h max: 35 / Limit h min: 1 / Limit k max: 35 / Limit k min: 1 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 1192257.53 / Observed criterion F min: 1.22 / Rmerge(I) obs: 0.071 / Net I/σ(I): 50.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 3.8 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 2REB

2reb


Resolution: 2.6→31.18 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1441 10.1 %random
Rwork0.213 ---
all-15280 --
obs-14222 93.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 46.0448 Å2 / ksol: 0.346144 e/Å3
Displacement parametersBiso max: 130.63 Å2 / Biso mean: 62.52 Å2 / Biso min: 28.84 Å2
Baniso -1Baniso -2Baniso -3
1--6.24 Å27.9 Å20 Å2
2---6.24 Å20 Å2
3---12.49 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.39 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 5 34 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg0
X-RAY DIFFRACTIONx_mcbond_it1.411.5
X-RAY DIFFRACTIONx_mcangle_it2.412
X-RAY DIFFRACTIONx_scbond_it2.172
X-RAY DIFFRACTIONx_scangle_it3.332.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.36615910.10.3314150.0291910157482.4
2.72-2.860.3451559.60.27314590.0281891161485.4
2.86-3.040.2861709.70.26915770.0221914174791.3
3.04-3.280.318180100.25716270.0241901180795.1
3.28-3.610.2691849.90.22716720.021896185697.8
3.61-4.130.24320210.80.19516710.0171908187398.2
4.13-5.20.20320310.60.15917040.0141921190799.2
5.2-31.180.25118810.20.21116560.0181945184494.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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