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- PDB-3c1d: X-ray crystal structure of RecX -

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Basic information

Entry
Database: PDB / ID: 3c1d
TitleX-ray crystal structure of RecX
ComponentsRegulatory protein recX
KeywordsRECOMBINATION / DNA BINDING PROTEIN / tandem repeats / helix-turn-helix / Cytoplasm / DNA damage / DNA repair / SOS response
Function / homology
Function and homology information


SOS response / regulation of DNA repair / DNA repair / cytoplasm
Similarity search - Function
Regulatory protein RecX / : / : / : / RecX, second three-helix domain / RecX, third three-helix domain / RecX, first three-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily ...Regulatory protein RecX / : / : / : / RecX, second three-helix domain / RecX, third three-helix domain / RecX, first three-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Regulatory protein RecX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsRagone, S. / Maman, J.D. / Furnham, N. / Pellegrini, L.
CitationJournal: Embo J. / Year: 2008
Title: Structural basis for inhibition of homologous recombination by the RecX protein.
Authors: Ragone, S. / Maman, J.D. / Furnham, N. / Pellegrini, L.
History
DepositionJan 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein recX
B: Regulatory protein recX


Theoretical massNumber of molelcules
Total (without water)36,9702
Polymers36,9702
Non-polymers00
Water5,603311
1
A: Regulatory protein recX


Theoretical massNumber of molelcules
Total (without water)18,4851
Polymers18,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein recX


Theoretical massNumber of molelcules
Total (without water)18,4851
Polymers18,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.549, 71.757, 74.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regulatory protein recX / Protein oraA


Mass: 18484.959 Da / Num. of mol.: 2 / Mutation: C113A, C118A
Source method: isolated from a genetically manipulated source
Details: The recombinant RecX protein was expressed with an N-terminal hexahistidine tag. The tag was removed by cleaveage with Prescission protease (GE Healthcare). Cleaveage left an extra Glycine ...Details: The recombinant RecX protein was expressed with an N-terminal hexahistidine tag. The tag was removed by cleaveage with Prescission protease (GE Healthcare). Cleaveage left an extra Glycine amino acid at the N-terminus of the protein.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recX, oraA / Plasmid: pEGT-10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P66000
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST AMINO ACID OF THE SEQUENCE (GLY) IS A LEFT-OVER OF THE PRESCISSION PROTEASE CLEAVAGE ...THE FIRST AMINO ACID OF THE SEQUENCE (GLY) IS A LEFT-OVER OF THE PRESCISSION PROTEASE CLEAVAGE SEQUENCE LEVLFQ/GP, THAT WAS FUSED TO THE N-TERMINUS OF THE PROTEIN, TO ALLOW REMOVAL OF THE HISTIDINE TAG.

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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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 4000, 0.2 M Sodium Acetate, 0.1 M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→16.5 Å / Num. all: 28281 / Num. obs: 28281 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4001 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→16.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.037 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1407 5 %RANDOM
Rwork0.18 ---
all0.182 27866 --
obs0.182 27866 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.963 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--1.25 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 0 311 2870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222622
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9533550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9175324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.57121.655139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21815477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561541
X-RAY DIFFRACTIONr_chiral_restr0.1030.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022065
X-RAY DIFFRACTIONr_nbd_refined0.2040.21316
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.221
X-RAY DIFFRACTIONr_mcbond_it0.821.51609
X-RAY DIFFRACTIONr_mcangle_it1.20122524
X-RAY DIFFRACTIONr_scbond_it2.3631149
X-RAY DIFFRACTIONr_scangle_it3.7974.51026
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 104 -
Rwork0.235 1918 -
all-2022 -
obs--97.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.13853.8008-5.54876.2881-5.55714.7221-0.1825-0.1631-0.49650.0852-0.1868-0.46930.51740.33390.3693-0.05710.0158-0.02850.0203-0.0288-0.029828.18525.08226.879
21.9737-0.8455-0.16084.4501-0.53878.54180.0757-0.093-0.1258-0.0963-0.0124-0.09420.4282-0.1769-0.0633-0.0548-0.0274-0.03340.0275-0.0065-0.070523.46327.00220.191
31.86830.3832-2.61882.2231-0.76877.42480.10570.00910.1783-0.05210.113-0.0611-0.4394-0.0442-0.2187-0.0654-0.02930.0095-0.0658-0.0306-0.04626.75837.807-0.081
49.19289.2203-2.946622.3802-9.543715.9023-0.1058-0.3221-0.0759-0.0539-0.0121-0.2267-0.55080.01680.1179-0.0598-0.02930.025-0.00770.07210.092340.54242.96-18.033
58.42223.3129-3.64764.337-0.206415.1919-0.12690.6959-0.1772-0.35660.242-0.1893-0.1830.0723-0.1151-0.0789-0.0310.0331-0.0812-0.0275-0.065633.05435.351-18.303
644.61726.8268-24.92818.152-5.411125.83470.8571.472.6335-0.7150.471.2332-1.3663-1.2493-1.32690.35420.13730.03110.12260.08420.323527.5642.68-17.522
74.44290.5395-3.40590.473-0.039610.49940.0301-0.3686-0.39490.0617-0.0987-0.11460.3381.34450.0687-0.02520.0475-0.01510.16910.0159-0.007830.56925.275-32.374
88.8793.6646-1.26677.3399-1.48435.46820.0380.2234-0.16880.0562-0.1434-0.7471-0.27430.4490.1054-0.040.0329-0.01480.02150.0233-0.05527.37631.826-35.471
91.46820.0753-0.36924.7152-6.533419.7317-0.00520.2508-0.1517-0.30920.0338-0.02550.9839-0.2681-0.0286-0.0358-0.0469-0.0109-0.025-0.036-0.05817.05920.95-16.128
102.16710.2829-0.47172.8799-3.79027.39850.1042-0.08660.0930.15020.19160.2374-0.323-0.4392-0.2958-0.0188-0.01730.0012-0.0104-0.0104-0.03215.97426.79-9.872
116.8871-0.17031.758913.3091-6.79369.479-0.16070.3321-0.3419-0.12460.68020.54720.8404-0.6658-0.51950.0943-0.0911-0.00670.08420.0410.040214.5499.7593.883
123.39471.04652.45918.5537-3.238412.01980.1764-0.3159-0.04570.67710.11770.20670.2842-0.5625-0.2941-0.0229-0.0362-0.0007-0.05560.0002-0.063218.23718.1028.058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 241 - 17
2X-RAY DIFFRACTION2AA25 - 7018 - 63
3X-RAY DIFFRACTION3AA71 - 12664 - 119
4X-RAY DIFFRACTION4AA127 - 135120 - 128
5X-RAY DIFFRACTION5AA136 - 154129 - 147
6X-RAY DIFFRACTION6AA155 - 161148 - 154
7X-RAY DIFFRACTION7BB8 - 451 - 38
8X-RAY DIFFRACTION8BB46 - 6839 - 61
9X-RAY DIFFRACTION9BB69 - 8762 - 80
10X-RAY DIFFRACTION10BB88 - 12081 - 113
11X-RAY DIFFRACTION11BB121 - 132114 - 125
12X-RAY DIFFRACTION12BB133 - 161126 - 154

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