- PDB-3mxn: Crystal structure of the RMI core complex -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3mxn
Title
Crystal structure of the RMI core complex
Components
RecQ-mediated genome instability protein 1
RecQ-mediated genome instability protein 2
Keywords
REPLICATION / Bloom syndrome / helicase / RMI / topoisomerase / Replication protein A
Function / homology
Function and homology information
regulation of sister chromatid segregation / reduction of food intake in response to dietary excess / RecQ family helicase-topoisomerase III complex / resolution of DNA recombination intermediates / maintenance of rDNA / resolution of meiotic recombination intermediates / Impaired BRCA2 binding to PALB2 / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function ...regulation of sister chromatid segregation / reduction of food intake in response to dietary excess / RecQ family helicase-topoisomerase III complex / resolution of DNA recombination intermediates / maintenance of rDNA / resolution of meiotic recombination intermediates / Impaired BRCA2 binding to PALB2 / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of double-strand break repair via homologous recombination / response to glucose / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / multicellular organism growth / glucose homeostasis / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / nuclear body / nuclear speck / nucleotide binding / DNA repair / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 10 mM Hepes pH 7.1, 0.05 M NaSCN, 20% ethylene glycol, 2 mM DTT, 13% polyethylene glycol 3350, with benzamidine (1%) added to the drop, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution: 1.55→1.58 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.378 / % possible all: 83
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Processing
Software
Name
Version
Classification
MAR345
datacollection
ARP/wARP
modelbuilding
REFMAC
5.5.0072
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.55→29.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.411 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23106
1966
5 %
RANDOM
Rwork
0.19548
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all
0.1972
40496
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obs
0.1972
37250
96.97 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 18.566 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.66 Å2
0 Å2
0 Å2
2-
-
0.09 Å2
0 Å2
3-
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-
0.57 Å2
Refinement step
Cycle: LAST / Resolution: 1.55→29.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2182
0
9
251
2442
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
2337
X-RAY DIFFRACTION
r_angle_refined_deg
1.191
2.002
3192
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.467
5
316
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.838
24.149
94
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.464
15
436
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.879
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.078
0.2
367
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
1756
X-RAY DIFFRACTION
r_mcbond_it
0.611
1.5
1473
X-RAY DIFFRACTION
r_mcangle_it
1.168
2
2403
X-RAY DIFFRACTION
r_scbond_it
1.877
3
864
X-RAY DIFFRACTION
r_scangle_it
3.181
4.5
771
LS refinement shell
Resolution: 1.55→1.59 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.366
130
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Rwork
0.314
2313
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obs
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84.3 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
0.3878
0.1068
0.1151
0.1277
0.0383
0.079
-0.0012
-0.0056
-0.0059
0.0079
0.0028
0.0039
-0.0079
0.001
-0.0017
0.0022
0
0.0005
0.0004
0.0003
0.0004
8.1832
0.4551
-10.1492
2
0.4841
-0.023
-0.0482
0.3512
0.074
0.3724
-0.0126
0.0409
-0.0468
-0.0468
0.027
-0.0109
0.0147
0.0239
-0.0144
0.009
-0.0024
0.001
0.009
-0.0074
0.0068
8.2492
-12.8349
-28.479
3
6.2915
-1.3068
-1.3795
9.7117
2.2487
0.7103
-0.1458
0.1272
-0.1986
0.3812
0.0232
0.3984
0.1057
-0.0186
0.1226
0.0167
-0.0003
0.0181
0.011
-0.0017
0.0198
-3.1622
-19.4957
-4.2208
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
476 - 625
2
X-RAY DIFFRACTION
2
B
20 - 148
3
X-RAY DIFFRACTION
3
A
1 - 232
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