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- PDB-2quw: Hammerhead Ribozyme G12A mutant after cleavage -

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Basic information

Entry
Database: PDB / ID: 2quw
TitleHammerhead Ribozyme G12A mutant after cleavage
Components(Hammerhead ribozyme, cleaved fragment) x 2
KeywordsRNA / Hammerhead ribozyme / ribozyme / catalytic RNA / ribozyme-product complex
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsChi, Y.I. / Scott, W.G. / Kim, S.H.
CitationJournal: Plos Biol. / Year: 2008
Title: Capturing hammerhead ribozyme structures in action by modulating general base catalysis.
Authors: Chi, Y.I. / Martick, M. / Lares, M. / Kim, R. / Scott, W.G. / Kim, S.H.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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 / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

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Assembly

Deposited unit
A: Hammerhead ribozyme, cleaved fragment
B: Hammerhead ribozyme, cleaved fragment
C: Hammerhead ribozyme, cleaved fragment
D: Hammerhead ribozyme, cleaved fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,25621
Polymers44,8424
Non-polymers41317
Water91951
1
A: Hammerhead ribozyme, cleaved fragment
B: Hammerhead ribozyme, cleaved fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,66412
Polymers22,4212
Non-polymers24310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-72 kcal/mol
Surface area11420 Å2
MethodPISA
2
C: Hammerhead ribozyme, cleaved fragment
D: Hammerhead ribozyme, cleaved fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5919
Polymers22,4212
Non-polymers1707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-52 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.030, 53.140, 72.050
Angle α, β, γ (deg.)74.240, 81.370, 75.650
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13B
23D
14B
24D
15B
25D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GGCCCCCCAA2 - 122 - 12
21GGCCCCCCCC2 - 122 - 12
12AAGGBB13 - 201 - 8
22AAGGDD13 - 201 - 8
13UUCCBB26 - 4214 - 30
23UUCCDD26 - 4214 - 30
14GGGGBB45 - 5933 - 47
24GGGGDD45 - 5933 - 47
15CCCCBB60 - 6448 - 52
25CCCCDD60 - 6448 - 52

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: RNA chain Hammerhead ribozyme, cleaved fragment


Mass: 4065.259 Da / Num. of mol.: 2 / Mutation: G13A / Source method: obtained synthetically / Details: in vitro T7 RNA polymerase transcription
#2: RNA chain Hammerhead ribozyme, cleaved fragment


Mass: 18355.914 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: first residue A13G mutation
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.22 Å3/Da / Density % sol: 44.66 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.46 Å / Num. all: 17539 / Num. obs: 15733 / % possible obs: 89.43 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementResolution: 2.2→19.46 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.94 / SU B: 22.613 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1806 10.3 %RANDOM
Rwork0.199 ---
obs0.205 17539 89.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.969 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å21.99 Å20.05 Å2
2---0.81 Å2-0.07 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2966 17 51 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213316
X-RAY DIFFRACTIONr_angle_refined_deg1.76235150
X-RAY DIFFRACTIONr_chiral_restr0.0790.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021430
X-RAY DIFFRACTIONr_nbd_refined0.1920.21189
X-RAY DIFFRACTIONr_nbtor_refined0.2770.22041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.28
X-RAY DIFFRACTIONr_scbond_it1.62834702
X-RAY DIFFRACTIONr_scangle_it2.6234.55150
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A237MEDIUM POSITIONAL0.530.5
1A237MEDIUM THERMAL0.712
2B170MEDIUM POSITIONAL0.290.5
2B170MEDIUM THERMAL0.642
3B359MEDIUM POSITIONAL0.250.5
3B359MEDIUM THERMAL0.592
4B332MEDIUM POSITIONAL0.410.5
4B332MEDIUM THERMAL0.552
5B100MEDIUM POSITIONAL0.280.5
5B100MEDIUM THERMAL0.772
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 122 -
Rwork0.362 1109 -
all-1231 -
obs--85.96 %
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)
10.12860.6120.09123.16541.00771.36980.0370.12840.17930.5101-0.0614-0.2971-0.43770.18120.02440.00660.1264-0.01470.0175-0.012-0.1531-4.6568-5.16721.8928
20.03030.0107-0.0880.1424-0.25910.6310.0796-0.046-0.01050.07190.05790.0154-0.02150.0552-0.13760.10420.0715-0.0001-0.020.0135-0.0552-5.873-8.16214.4252
30.4107-0.18160.66360.76070.38722.47110.1956-0.15270.01240.2873-0.1075-0.04140.41740.0296-0.0881-0.03360.0493-0.0168-0.11770.0102-0.08787.3295-31.41632.7715
40.07370.0510.33460.06480.31591.7607-0.0154-0.0650.0199-0.0418-0.03420.0220.0223-0.17040.04960.2150.013-0.01740.0606-0.0009-0.05227.1801-28.355820.7168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 121 - 12
2X-RAY DIFFRACTION2BB13 - 691 - 57
3X-RAY DIFFRACTION3CC1 - 121 - 12
4X-RAY DIFFRACTION4DD13 - 691 - 57

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