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- PDB-6l8u: Crystal structure of human BCDIN3D in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6l8u
TitleCrystal structure of human BCDIN3D in complex with SAH
ComponentsRNA 5'-monophosphate methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


: / negative regulation of pre-miRNA processing / tRNA methyltransferase activity / miRNA metabolic process / RNA methyltransferase activity / RNA methylation / tRNA methylation / O-methyltransferase activity / MicroRNA (miRNA) biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases ...: / negative regulation of pre-miRNA processing / tRNA methyltransferase activity / miRNA metabolic process / RNA methyltransferase activity / RNA methylation / tRNA methylation / O-methyltransferase activity / MicroRNA (miRNA) biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
RNA methyltransferase bin3, C-terminal / Bin3-type S-adenosyl-L-methionine binding domain / RNA methyltransferase Bin3-like / Bicoid-interacting protein 3 (Bin3) / Bin3-type S-adenosyl-L-methionine (SAM) domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA 5'-monophosphate methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.925 Å
AuthorsLiu, Y. / Martinez, A. / Yamashita, S. / Tomita, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceLS135 Japan
Japan Society for the Promotion of Science18H03980 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26113002 Japan
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.
Authors: Liu, Y. / Martinez, A. / Yamashita, S. / Tomita, K.
History
DepositionNov 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 25, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA 5'-monophosphate methyltransferase
B: RNA 5'-monophosphate methyltransferase
C: RNA 5'-monophosphate methyltransferase
D: RNA 5'-monophosphate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3438
Polymers129,8054
Non-polymers1,5384
Water1267
1
A: RNA 5'-monophosphate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8362
Polymers32,4511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA 5'-monophosphate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8362
Polymers32,4511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA 5'-monophosphate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8362
Polymers32,4511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA 5'-monophosphate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8362
Polymers32,4511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.140, 140.340, 86.420
Angle α, β, γ (deg.)90.000, 105.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA 5'-monophosphate methyltransferase / BCDIN3 domain-containing protein


Mass: 32451.363 Da / Num. of mol.: 4 / Fragment: UNP residues 14-284 / Mutation: delta_1-13, delta_92-99, delta_285-294
Source method: isolated from a genetically manipulated source
Details: The N-terminal "MGSSHHHHHHSSGLVPRGSHM" is the expression tag derived from pET15b vector. The residues 1-13, 92-99, and 285-292 were truncated from full-length hBCDIN3D for structural analysis.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCDIN3D / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7Z5W3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 200 mM CaCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.925→41.65 Å / Num. obs: 23888 / % possible obs: 99.7 % / Redundancy: 9.161 % / Biso Wilson estimate: 44.61 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.217 / Χ2: 0.991 / Net I/σ(I): 8.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.93-38.8662.3731.115826180217850.6582.51799.1
3-3.089.521.8161.5316080168616890.7961.92100
3.08-3.179.3561.4111.9215728168616810.8671.49499.7
3.17-3.279.2160.9242.6914773160616030.9390.97999.8
3.27-3.388.8420.6563.6514015158215850.9610.697100
3.38-3.58.7450.5644.2913292152915200.9690.59999.4
3.5-3.639.0840.435.4313381147114730.9790.456100
3.63-3.789.610.3357.0213636142514190.9890.35499.6
3.78-3.949.6060.2598.3312978134813510.9920.274100
3.94-4.149.560.2189.6712419130312990.9940.23199.7
4.14-4.369.3130.17811.3311734126512600.9950.18999.6
4.36-4.629.1810.14512.8310310112211230.9960.154100
4.62-4.948.6540.12514.49589111811080.9960.13499.1
4.94-5.348.4830.13114.288780103710350.9950.1499.8
5.34-5.859.6160.13414.5390209349380.9930.142100
5.85-6.549.6630.13114.1281758508460.9950.13899.5
6.54-7.559.3930.10117.7970737557530.9960.10799.7
7.55-9.258.7750.0821.557216516520.9940.085100
9.25-13.088.2440.06924.440814974950.9960.07499.6
13.08-41.658.1250.06824.3122182892730.9950.07394.5

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_1309refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UNA

5una


Resolution: 2.925→41.65 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 978 4.99 %
Rwork0.2119 19706 -
obs0.2148 20740 86.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.28 Å2 / Biso mean: 46.3074 Å2 / Biso min: 7.3 Å2
Refinement stepCycle: final / Resolution: 2.925→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 104 7 7482
Biso mean--29.36 29.2 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057702
X-RAY DIFFRACTIONf_angle_d0.85610439
X-RAY DIFFRACTIONf_chiral_restr0.051114
X-RAY DIFFRACTIONf_plane_restr0.0081340
X-RAY DIFFRACTIONf_dihedral_angle_d21.8522848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9255-3.07960.32811020.2943184657
3.0796-3.27250.35331170.2754229371
3.2725-3.52510.32981390.2317267883
3.5251-3.87960.29681670.2138313297
3.8796-4.44040.24261710.19513242100
4.4404-5.59230.24081690.1883242100
5.5923-41.650.22931690.1988327399

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