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- PDB-1u94: Crystal Structure of E. Coli RecA in a Compressed Helical Filamen... -

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Basic information

Entry
Database: PDB / ID: 1u94
TitleCrystal Structure of E. Coli RecA in a Compressed Helical Filament Form 2
ComponentsRecA protein
KeywordsDNA BINDING PROTEIN / RecA / homologous 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Aug 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)38,4194
Polymers38,2991
Non-polymers1203
Water4,990277
1
A: RecA protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)230,51324
Polymers229,7916
Non-polymers72118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z+1/31
crystal symmetry operation3_465-x+y-1,-x+1,z+2/31
crystal symmetry operation4_575-x,-y+2,z+1/21
crystal symmetry operation5_455y-1,-x+y,z+5/61
crystal symmetry operation6_665x-y+1,x+1,z+1/61
Unit cell
Length a, b, c (Å)105.854, 105.854, 73.496
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 550 MME, calcium chloride, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: SBC-2 / Detector: CCD / Date: Jul 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→34.65 Å / Num. all: 36951 / Num. obs: 35211 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 16.7 Å2 / Limit h max: 48 / Limit h min: 0 / Limit k max: 47 / Limit k min: 0 / Limit l max: 38 / Limit l min: 0 / Observed criterion F max: 519862.03 / Observed criterion F min: 0.45 / Rmerge(I) obs: 0.079 / Net I/σ(I): 36.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

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

2reb


Resolution: 1.9→34.65 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3496 9.9 %random
Rwork0.187 ---
all-36951 --
obs-35211 95.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 54.5433 Å2 / ksol: 0.368018 e/Å3
Displacement parametersBiso max: 117.84 Å2 / Biso mean: 30.75 Å2 / Biso min: 10.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å22.16 Å20 Å2
2---0.86 Å20 Å2
3---1.72 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 3 277 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg22.7
X-RAY DIFFRACTIONx_torsion_impr_deg0
X-RAY DIFFRACTIONx_mcbond_it3.41.5
X-RAY DIFFRACTIONx_mcangle_it4.262
X-RAY DIFFRACTIONx_scbond_it5.832
X-RAY DIFFRACTIONx_scangle_it7.982.5
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 (%)
1.9-1.990.2953929.90.26535820.0154627397485.9
1.99-2.090.2545310.50.2238480.0124598430193.5
2.09-2.220.231442100.19739680.0114630441095.2
2.22-2.40.2444129.50.20139360.0124583434894.9
2.4-2.640.2174079.10.17740540.0114625446196.5
2.64-3.020.22548210.70.18640340.014615451697.9
3.02-3.80.20547010.20.17941310.0094629460199.4
3.8-34.650.2064389.50.17141620.014698460097.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.TOP

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