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- PDB-1xp8: Deinococcus radiodurans RecA in complex with ATP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 1xp8
TitleDeinococcus radiodurans RecA in complex with ATP-gamma-S
ComponentsRecA protein
KeywordsDNA BINDING PROTEIN / Recombination / Radioresistance / DNA-repair / ATPase / DNA-binding protein
Function / homology
Function and homology information


SOS response / ATP-dependent activity, acting on DNA / double-strand break repair / single-stranded DNA binding / DNA recombination / damaged DNA binding / ATP binding / cytoplasm
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / 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 protein, C-terminal domain / Rec A Protein; domain 2 / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Protein RecA
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBell, C.E. / Rajan, R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of RecA from Deinococcus radiodurans: insights into the structural basis of extreme radioresistance.
Authors: Rajan, R. / Bell, C.E.
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Non-polymer description
Revision 1.4Sep 5, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Aug 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

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Assembly

Deposited unit
A: RecA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9942
Polymers38,4711
Non-polymers5231
Water48627
1
A: RecA protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)233,96512
Polymers230,8266
Non-polymers3,1396
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)111.380, 111.380, 67.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological assembly is a 6sub1-symmetric helical filament with undefined length generated by the P61 crystal symmetry

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Components

#1: Protein RecA protein / / Recombinase A


Mass: 38470.957 Da / Num. of mol.: 1 / Fragment: RecA with N-terminal GSH residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: recA / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P42443
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.2 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: PEG 4000, ammonium acetate, calcium chloride, Mes, pH 8.0, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 18, 2004 / Details: Osmic Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→27.65 Å / Num. all: 16644 / Num. obs: 16644 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 12.1 Å2 / Limit h max: 38 / Limit h min: 0 / Limit k max: 38 / Limit k min: 0 / Limit l max: 27 / Limit l min: 0 / Observed criterion F max: 1920538.11 / Observed criterion F min: 31.1 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1648 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2REB

2reb


Resolution: 2.5→27.65 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1705 10.3 %random
Rwork0.228 ---
all-16618 --
obs-16582 99.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.0538 Å2 / ksol: 0.346676 e/Å3
Displacement parametersBiso max: 86.58 Å2 / Biso mean: 48.68 Å2 / Biso min: 23.64 Å2
Baniso -1Baniso -2Baniso -3
1--7.73 Å27.47 Å20 Å2
2---7.73 Å20 Å2
3---15.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.46 Å
Luzzati d res high-2.5
Refinement stepCycle: LAST / Resolution: 2.5→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 31 27 2282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.6
X-RAY DIFFRACTIONx_torsion_impr_deg0
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 (%)
2.5-2.610.35621810.60.34518350.0242060205399.7
2.61-2.750.32921710.60.30118240.0222047204199.7
2.75-2.920.3261939.30.28918890.02320822082100
2.92-3.150.27721010.20.25718480.01920592058100
3.15-3.470.29621910.60.23418560.0220752075100
3.47-3.970.25221110.10.21218810.01720922092100
3.97-4.990.22721810.50.18618610.0152085207999.7
4.99-27.650.2121910.40.19318830.0142133210298.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3SAP_PRODRG.PARAMSAP_PRODRG.TOP
X-RAY DIFFRACTION4CIS_157.PARAM

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