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- PDB-3g96: Crystal structure of the Bacillus anthracis glmS ribozyme bound t... -

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Basic information

Entry
Database: PDB / ID: 3g96
TitleCrystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P
Components
  • GLMS RIBOZYME
  • RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
KeywordsRNA binding protein/RNA / catalytic RNA / RNA binding protein-RNA COMPLEX
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6MN / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
syntetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.01 Å
AuthorsStrobel, S.A. / Cochrane, J.C. / Lipchock, S.V. / Smith, K.D.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme
Authors: Cochrane, J.C. / Lipchock, S.V. / Smith, K.D. / Strobel, S.A.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 7, 2018Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Apr 11, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_beamline / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.8Feb 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: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
E: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
P: GLMS RIBOZYME
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
Q: GLMS RIBOZYME
C: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
R: GLMS RIBOZYME
D: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
H: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
S: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,04922
Polymers244,57112
Non-polymers47810
Water2,414134
1
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
E: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
P: GLMS RIBOZYME


Theoretical massNumber of molelcules
Total (without water)61,1433
Polymers61,1433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
Q: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4757
Polymers61,1433
Non-polymers3324
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
R: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2899
Polymers61,1433
Non-polymers1466
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
H: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
S: GLMS RIBOZYME


Theoretical massNumber of molelcules
Total (without water)61,1433
Polymers61,1433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.401, 232.369, 104.657
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13E
23H
14F
24G
15P
25S
16Q
26R

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 905 - 90
21DD5 - 905 - 90
12BB5 - 905 - 90
22CC5 - 905 - 90
13EE1 - 131 - 13
23HH1 - 131 - 13
14FF1 - 131 - 13
24GG1 - 131 - 13
15PP1 - 1411 - 141
25SS1 - 1411 - 141
16QQ1 - 1411 - 141
26RR1 - 1411 - 141

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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RNA chain , 2 types, 8 molecules EFGHPQRS

#2: RNA chain
RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')


Mass: 4177.608 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) syntetic construct (others)
#3: RNA chain
GLMS RIBOZYME


Mass: 45624.859 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: in vitro transcribed from a DNA template / Source: (synth.) syntetic construct (others)

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A


Mass: 11340.315 Da / Num. of mol.: 4 / Fragment: RNA BINDING DOMAIN (UNP residues 1 to 98) / Mutation: Y31H,Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: SNRPA / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09012
#4: Sugar ChemComp-6MN / 2-amino-2-deoxy-6-O-phosphono-alpha-D-mannopyranose / Mannosamine-6-phosphate / 6-O-phosphono-alpha-D-mannosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-mannose / 2-amino-2-deoxy-6-O-phosphono-D-mannose / 2-amino-2-deoxy-6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO8P
IdentifierTypeProgram
a-D-ManpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 143 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: Si(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 41443 / % possible obs: 92.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.14 / Χ2: 1.03 / Net I/σ(I): 8.471
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.113.90.77940230.984190.6
3.11-3.233.90.38540261.046191
3.23-3.383.90.30440481.049189.5
3.38-3.563.90.30240331.05192
3.56-3.783.90.21240751.029191.5
3.78-4.073.80.16941141.044192.2
4.07-4.483.80.15441641.025193.8
4.48-5.133.90.13342241.037194.3
5.13-6.463.90.12243351.045196.7
6.46-5040.09644010.999197.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 3.01→34.75 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / SU B: 27.425 / SU ML: 0.516 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.624 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.311 2127 5.1 %RANDOM
Rwork0.255 ---
obs0.258 41406 92.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 134.89 Å2 / Biso mean: 80.025 Å2 / Biso min: 25.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å2-1.06 Å2
2---1.24 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 3.01→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 13081 25 134 16104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.02117597
X-RAY DIFFRACTIONr_bond_other_d00.027826
X-RAY DIFFRACTIONr_angle_refined_deg0.7332.84526731
X-RAY DIFFRACTIONr_angle_other_deg1.697319612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9875360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.79323.636132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9715564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1351520
X-RAY DIFFRACTIONr_chiral_restr0.0370.23504
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.029481
X-RAY DIFFRACTIONr_gen_planes_other00.021974
X-RAY DIFFRACTIONr_mcbond_it0.1421.51819
X-RAY DIFFRACTIONr_mcbond_other0.011.5748
X-RAY DIFFRACTIONr_mcangle_it0.25922930
X-RAY DIFFRACTIONr_scbond_it0.458315778
X-RAY DIFFRACTIONr_scangle_it0.8194.523801
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1313MEDIUM POSITIONAL0.350.5
1A1313MEDIUM THERMAL0.032
2B1312MEDIUM POSITIONAL0.250.5
2B1312MEDIUM THERMAL0.042
3E366MEDIUM POSITIONAL0.20.5
3E366MEDIUM THERMAL0.062
4F385MEDIUM POSITIONAL0.390.5
4F385MEDIUM THERMAL0.092
5P4121MEDIUM POSITIONAL0.240.5
5P4121MEDIUM THERMAL0.052
6Q4164MEDIUM POSITIONAL0.240.5
6Q4164MEDIUM THERMAL0.092
LS refinement shellResolution: 3.007→3.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 166 -
Rwork0.37 2587 -
all-2753 -
obs--83.86 %

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