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- PDB-3zd5: THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERH... -

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Basic information

Entry
Database: PDB / ID: 3zd5
TitleTHE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME
Components
  • HAMMERHEAD RIBOZYME, ENZYME STRAND
  • HAMMERHEAD RIBOZYME, SUBSTRATE STRAND
KeywordsRNA / CATALYTIC RNA / IN-LINE ATTACK / HAMMERHEAD RNA / STEM-LOOP INTERACTION / URIDINE TURN / A-FORM HELIX
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMartick, M. / Scott, W.G.
CitationJournal: Cell / Year: 2006
Title: Tertiary contacts distant from the active site prime a ribozyme for catalysis.
Authors: Martick, M. / Scott, W.G.
History
DepositionNov 24, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionDec 12, 2012ID: 2GOZ
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Other
Revision 1.2Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAMMERHEAD RIBOZYME, ENZYME STRAND
B: HAMMERHEAD RIBOZYME, SUBSTRATE STRAND


Theoretical massNumber of molelcules
Total (without water)20,4332
Polymers20,4332
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-2 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.886, 69.210, 60.076
Angle α, β, γ (deg.)90.00, 111.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain HAMMERHEAD RIBOZYME, ENZYME STRAND


Mass: 13941.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ENZYME STRAND WAS OBTAINED BY T7 RNA TRANSCRIPTION / Source: (synth.) Schistosoma mansoni
#2: RNA chain HAMMERHEAD RIBOZYME, SUBSTRATE STRAND


Mass: 6491.608 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SUBSTRATE STRAND WAS OBTAINED BY SOLID-PHASE CHEMICAL SYNTHESIS
Source: (synth.) Schistosoma mansoni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE (OMC): CLEAVAGE SITE SUBSTRATE ANALOGUE INHIBITOR GUANOSINE-5'- ...O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE (OMC): CLEAVAGE SITE SUBSTRATE ANALOGUE INHIBITOR GUANOSINE-5'-DIPHOSPHATE (GDP): 5 PRIME END OF TRANSCRIBED SEQUENCE. 5-BROMO-URIDINE-5'-MONOPHOSPHATE (5BU): USED FOR MAD PHASING

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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: 47.78 % / Description: ALL VALUES SAME AS 2GOZ
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop
Details: THE ENZYME AND SUBSTRATE WERE MIXED IN EQUIMOLAR AMOUNTS IN A SOLUTION CONTAINING 50 MM MES PH 5.5, 1.5 MM EDTA. THE COMPLEX WAS FORMED BY INCUBATING THE MIXTURE AT 95C FOR 2 MIN., THEN AT ...Details: THE ENZYME AND SUBSTRATE WERE MIXED IN EQUIMOLAR AMOUNTS IN A SOLUTION CONTAINING 50 MM MES PH 5.5, 1.5 MM EDTA. THE COMPLEX WAS FORMED BY INCUBATING THE MIXTURE AT 95C FOR 2 MIN., THEN AT 65C FOR 2 MIN., AND FINALLY AT 27C FOR 5 MIN. 1 MM MGCL2 WAS INCLUDED IN THE MIXTURE BEFORE THE FINAL INCUBATION STEP. A 10 MG/ML CONCENTRATION OF RNA WAS USED FOR THE CRYSTALLIZATION EXPERIMENTS. THE RESERVOIR SOLUTION CONTAINED 0.5M (NH4)2SO4, 100 MM MES PH 6.5, AND 35% PEG 3350. AFTER MIXING THE RESERVOIR SOLUTION, THE SALT AND PEG PHASES WERE ALLOWED TO SEPARATE, AND ONLY THE SALT PHASE WAS USED FOR THE DROPS. THE CRYSTALS GREW IN HANGING DROPS OF 2 MICROLITERS AFTER 12 MONTHS OF INCUBATION AT 28C. THE CRYSTALS WERE WASHED IN THE SALT PHASE OF THE RESERVOIR SOLUTION PRIOR TO CRYO-FREEZING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.919, 0.920, 0.9266
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9191
20.921
30.92661
ReflectionResolution: 2.2→55.73 Å / Num. obs: 9712 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 43.18 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
ADSCdata reduction
MOSFLMdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20.22 Å / SU ML: 0.27 / σ(F): 1.5 / Phase error: 25.51 / Stereochemistry target values: ML
Details: TLS MODEL BASED ON OUTPUT FROM TLS MOTION DETERMINATION SERVER. TO REPLACE 2GOZ COORDINATES (DATA REMAIN THE SAME). CORRECTED ANTI TO SYN BASE CONFORMATION OF C8 IN CHAIN A. IMPROVED TLS AND WATER MODELS
RfactorNum. reflection% reflection
Rfree0.2117 935 9.7 %
Rwork0.1768 --
obs0.1805 9615 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→20.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1346 0 34 1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051503
X-RAY DIFFRACTIONf_angle_d0.9372337
X-RAY DIFFRACTIONf_dihedral_angle_d15.306744
X-RAY DIFFRACTIONf_chiral_restr0.039309
X-RAY DIFFRACTIONf_plane_restr0.00663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2004-2.31620.3061410.24411246X-RAY DIFFRACTION100
2.3162-2.46110.27351440.23661217X-RAY DIFFRACTION100
2.4611-2.65070.30871240.24681255X-RAY DIFFRACTION100
2.6507-2.91680.31151160.2531247X-RAY DIFFRACTION100
2.9168-3.33720.25041350.19291254X-RAY DIFFRACTION99
3.3372-4.19830.19941370.1471239X-RAY DIFFRACTION99
4.1983-20.22090.1331380.12731222X-RAY DIFFRACTION97
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)
14.25253.7274-1.44495.9746-4.30638.1616-0.0481-0.2587-0.2765-0.2380.59560.12841.479-0.2624-0.6610.5529-0.0185-0.02030.4116-0.0640.3284-9.476218.869811.7237
20.11852.19360.8113.49352.03120.0587-0.02960.0249-0.1988-0.5860.15-0.8705-0.22720.1963-0.13330.3748-0.02080.07320.3427-0.01660.4996-11.23357.2618-8.4889
31.161-1.49150.21450.88350.89481.4751-0.26760.37540.40360.10560.2926-0.2755-0.43680.7151-0.07770.6297-0.17790.03220.69930.04330.5237-18.236810.2441-21.6235
44.393-1.4466-1.00171.2620.6215.5628-0.6095-1.4966-0.07460.901-0.4580.0125-0.1193-1.09440.6970.4701-0.14010.05220.6644-0.03780.672-18.204115.7910.2597
57.7184-1.88082.49622.07650.56373.29160.29710.1801-0.69820.18520.07970.5144-0.9466-0.6731-0.16710.39560.0378-0.10720.6957-0.05820.4378-22.882113.9208-9.7629
63.70461.19761.22423.6976-2.09812.577-0.7316-0.36740.4529-0.03150.2016-0.2399-1.7445-0.75440.51460.9536-0.001-0.14770.59020.06820.5295-23.817817.1293-25.1717
71.9145-1.24490.73252.35120.19032.0369-0.24030.2234-0.0918-0.39270.12050.022-0.04390.53540.07810.5127-0.02120.04210.44670.0750.3924-31.7087.8629-33.0374
80.507-1.04760.31180.818-0.67561.2216-0.37770.14730.2175-0.05350.1307-0.194-0.6890.08620.09670.6174-0.0624-0.03210.45160.04050.3581-30.565812.8975-25.8106
9-0.1116-0.33280.01033.0746-0.2820.61620.0456-0.19050.44180.5737-0.4214-0.46820.047-0.04050.39550.4262-0.058-0.03830.37670.04740.5244-14.92242.3326-3.8181
102.0548-0.7013-1.34731.73381.45343.9355-0.06340.0029-0.50530.0372-0.0266-0.11750.8374-0.0763-0.01510.4093-0.0295-0.02150.350.0490.4702-0.228222.15639.4133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:14)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 15:25)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 26:30)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 31:34)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 35:38)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 39:43)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:7)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 8:15)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 16:20)

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