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- PDB-5af0: MAEL domain from Bombyx mori Maelstrom -

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Basic information

Entry
Database: PDB / ID: 5af0
TitleMAEL domain from Bombyx mori Maelstrom
ComponentsMAELSTROM
KeywordsUNKNOWN PROTEIN / MAEL / PIRNA / RIBONUCLEASE / FUSION PROTEIN / PIWI
Function / homology
Function and homology information


regulation of miRNA-mediated gene silencing / multicellular organism development / regulatory ncRNA-mediated gene silencing / meiotic cell cycle / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Maelstrom domain / Protein maelstrom / piRNA pathway germ-plasm component / HMG-box domain / HMG boxes A and B DNA-binding domains profile. / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
Maelstrom / HMG box domain-containing protein
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsChen, K. / Campbell, E. / Pandey, R.R. / Yang, Z. / McCarthy, A.A. / Pillai, R.S.
CitationJournal: RNA / Year: 2015
Title: Metazoan Maelstrom is an RNA-Binding Protein that Has Evolved from an Ancient Nuclease Active in Protists.
Authors: Chen, K. / Campbell, E. / Pandey, R.R. / Yang, Z. / Mccarthy, A.A. / Pillai, R.S.
History
DepositionJan 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: MAELSTROM
B: MAELSTROM
C: MAELSTROM
D: MAELSTROM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6588
Polymers119,3964
Non-polymers2624
Water63135
1
A: MAELSTROM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9142
Polymers29,8491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MAELSTROM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9142
Polymers29,8491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MAELSTROM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9142
Polymers29,8491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MAELSTROM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9142
Polymers29,8491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.370, 101.210, 101.640
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MAELSTROM


Mass: 29848.975 Da / Num. of mol.: 4 / Fragment: MAEL DOMAIN, RESIDUES 78-159 AND 160-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Cell: OVARIAN / Cell line: BMN4 / Plasmid: PETM-11SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: H9JFX7, UniProt: A0A0H5AXR2*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.25 Å3/Da / Density % sol: 62 %
Description: DATA COLLECTED USING THE OSCILLATION FINE SLICING METHOD.
Crystal growpH: 7 / Details: 3.5M SODIUM FORMATE, PH=7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 58899 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SCALEPACKdata scaling
CRANK2phasing
PHASERphasing
PHENIXdev_1839refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.401→45.416 Å / σ(F): 1.35 / Phase error: 37.13 / Stereochemistry target values: TWIN_LSQ_F
Details: THE FOLLOWING RESIDUES ARE DISORDERED. MOLA IS MISSING 78-89, 281-284, AND 335-338. MOLB IS MISSING 78- 88, 280-284, AND 335-338. MOLC IS MISSING 78-86, 184-186, 260- 261, 281-285, AND 335- ...Details: THE FOLLOWING RESIDUES ARE DISORDERED. MOLA IS MISSING 78-89, 281-284, AND 335-338. MOLB IS MISSING 78- 88, 280-284, AND 335-338. MOLC IS MISSING 78-86, 184-186, 260- 261, 281-285, AND 335-338. MOLD IS MISSING 78-85, 184-189, 283- 285, AND 335-338.
RfactorNum. reflection% reflection
Rfree0.2627 2928 5 %
Rwork0.2265 --
obs0.2305 58088 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→45.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7258 0 4 35 7297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127426
X-RAY DIFFRACTIONf_angle_d1.47610076
X-RAY DIFFRACTIONf_dihedral_angle_d15.3882623
X-RAY DIFFRACTIONf_chiral_restr0.0611165
X-RAY DIFFRACTIONf_plane_restr0.0081310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4016-2.4430.43151490.40152757X-RAY DIFFRACTION91
2.443-2.48730.40931460.38912753X-RAY DIFFRACTION92
2.4873-2.53510.41471340.37112725X-RAY DIFFRACTION92
2.5351-2.58680.40281320.37112722X-RAY DIFFRACTION92
2.5868-2.6430.37691240.35482700X-RAY DIFFRACTION92
2.643-2.70440.38251520.34662675X-RAY DIFFRACTION89
2.7044-2.7720.30311560.31492687X-RAY DIFFRACTION91
2.772-2.84690.33981140.29972773X-RAY DIFFRACTION93
2.8469-2.93050.33031410.28392775X-RAY DIFFRACTION92
2.9305-3.0250.27181240.27862767X-RAY DIFFRACTION93
3.025-3.13290.27581480.26722737X-RAY DIFFRACTION93
3.1329-3.25810.28421320.24362760X-RAY DIFFRACTION92
3.2581-3.4060.26091810.2322716X-RAY DIFFRACTION91
3.406-3.58510.26381590.21652777X-RAY DIFFRACTION93
3.5851-3.80910.25511490.19112759X-RAY DIFFRACTION93
3.8091-4.1020.20221380.1782812X-RAY DIFFRACTION94
4.102-4.51280.2061820.1662744X-RAY DIFFRACTION91
4.5128-5.1610.19661350.17172811X-RAY DIFFRACTION94
5.161-6.48440.25011400.18762840X-RAY DIFFRACTION94
6.4844-25.41140.21851340.18122871X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 110.6921 Å / Origin y: -2.9609 Å / Origin z: 71.1813 Å
111213212223313233
T0.4082 Å20.0054 Å20 Å2-0.0527 Å20.0094 Å2--0.4377 Å2
L0.6478 °20.036 °2-0.0429 °2-0.0161 °20.0615 °2--0.6148 °2
S-0.0848 Å °-0.0978 Å °0.0399 Å °-0.0192 Å °-0.0408 Å °0.0315 Å °0.031 Å °0.1384 Å °0.1019 Å °
Refinement TLS groupSelection details: ALL

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