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- PDB-5jrj: Crystal Structure of Herbaspirillum seropedicae RecA -

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Basic information

Entry
Database: PDB / ID: 5jrj
TitleCrystal Structure of Herbaspirillum seropedicae RecA
ComponentsProtein RecA
KeywordsDNA BINDING PROTEIN / DNA-binding protein / ATP-dependent DNA protein / ATPase activity / DNA strand exchange
Function / homology
Function and homology information


SOS response / ATP-dependent activity, acting on DNA / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / ATP binding / metal ion 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesHerbaspirillum seropedicae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLeite, W.C. / Galvao, C.W. / Saab, S.C. / Iulek, J. / Etto, R.M. / Steffens, M.B.R. / Chitteni-Pattu, S. / Stanage, T. / Keck, J.L. / Cox, M.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32335 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098885 United States
CitationJournal: PLoS ONE / Year: 2016
Title: Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament.
Authors: Leite, W.C. / Galvao, C.W. / Saab, S.C. / Iulek, J. / Etto, R.M. / Steffens, M.B. / Chitteni-Pattu, S. / Stanage, T. / Keck, J.L. / Cox, M.M.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein RecA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4914
Polymers37,5171
Non-polymers9743
Water5,855325
1
A: Protein RecA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)230,94624
Polymers225,0996
Non-polymers5,84718
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)87.410, 87.410, 91.353
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
SymmetryHelical symmetry: (Dyad axis: no)

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Components

#1: Protein Protein RecA / Recombinase A


Mass: 37516.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum seropedicae (bacteria) / Strain: SmR1 / Cell: Proteobacteria / Gene: recA / Production host: Escherichia coli (E. coli) / Strain (production host): STL2669 / References: UniProt: Q9F672, UniProt: D8IYL4*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.69 Å3/Da / Density % sol: 54.2 % / Description: rodlike
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Single crystals were obtained with 0.25 M CaCl2 and 14% w/v PEG 3350 with addition of Polypropylene glycol P 400 (PPG 400) onto the drop to give a final concentration of 5-8% w/v.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→31.578 Å / Num. obs: 42574 / % possible obs: 97.67 % / Redundancy: 5.18 % / Biso Wilson estimate: 16.94 Å2 / Rmerge(I) obs: 0.0467 / Net I/σ(I): 31.03
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.6285 / Mean I/σ(I) obs: 2.08 / % possible all: 79.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PROTEUM PLUSVersion 2010.5data reduction
PROTEUM PLUSVersion 2010.5data scaling
PHASERPhaser-2.6.0phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XMV

1xmv


Resolution: 1.7→31.578 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 22.78
RfactorNum. reflection% reflection
Rfree0.2107 2024 4.75 %
Rwork0.1755 --
obs0.1772 42571 97.66 %
Solvent computationShrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 325 2644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152453
X-RAY DIFFRACTIONf_angle_d1.6213326
X-RAY DIFFRACTIONf_dihedral_angle_d15.553947
X-RAY DIFFRACTIONf_chiral_restr0.089384
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6996-1.74210.421090.33482252X-RAY DIFFRACTION76
1.7421-1.78920.30231400.2672732X-RAY DIFFRACTION92
1.7892-1.84180.26411490.22492959X-RAY DIFFRACTION100
1.8418-1.90130.23371480.19892954X-RAY DIFFRACTION100
1.9013-1.96920.22511500.18542935X-RAY DIFFRACTION100
1.9692-2.0480.21551500.18372958X-RAY DIFFRACTION100
2.048-2.14120.22191440.18232963X-RAY DIFFRACTION100
2.1412-2.25410.22361430.17112945X-RAY DIFFRACTION100
2.2541-2.39530.22671470.1692962X-RAY DIFFRACTION100
2.3953-2.58010.20311500.17962966X-RAY DIFFRACTION100
2.5801-2.83960.1991490.17262949X-RAY DIFFRACTION100
2.8396-3.25020.18751470.16422985X-RAY DIFFRACTION100
3.2502-4.09350.18981480.15152971X-RAY DIFFRACTION100
4.0935-31.58350.18551500.15843016X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 33.1732 Å / Origin y: 42.221 Å / Origin z: 42.1896 Å
111213212223313233
T0.1007 Å20.0138 Å2-0.0012 Å2-0.1118 Å20.0134 Å2--0.1049 Å2
L0.593 °2-0.0706 °20.2769 °2-0.2343 °2-0.1199 °2--0.1438 °2
S-0.0415 Å °0.0115 Å °0.0712 Å °-0.0202 Å °-0.0013 Å °-0.0108 Å °-0.0467 Å °0.0006 Å °-0.0319 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or ( chain A and resid 401 )A6 - 825
2X-RAY DIFFRACTION1chain A or ( chain A and resid 401 )A401

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