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- PDB-1qmh: Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiqui... -

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Basic information

Entry
Database: PDB / ID: 1qmh
TitleCrystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
ComponentsRNA 3'-TERMINAL PHOSPHATE CYCLASE
KeywordsLIGASE / 2'3'CYCLIC PHOSPHATE RNA
Function / homology
Function and homology information


RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm
Similarity search - Function
RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily ...RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Dihydrodipicolinate Reductase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL / RNA 3'-terminal phosphate cyclase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPalm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A.
CitationJournal: Structure / Year: 2000
Title: Crystal Structure of RNA 3'-Terminal Phosphate Cyclase, a Ubiquitous Enzyme with Unusual Topology
Authors: Palm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A.
History
DepositionSep 28, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA 3'-TERMINAL PHOSPHATE CYCLASE
B: RNA 3'-TERMINAL PHOSPHATE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5835
Polymers74,0282
Non-polymers5543
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10.8 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.800, 133.500, 51.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.515842, -0.671843, -0.531539), (-0.689428, -0.042742, 0.723092), (-0.508523, 0.739459, -0.44114)
Vector: 148.35341, 113.33745, -10.30362)

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Components

#1: Protein RNA 3'-TERMINAL PHOSPHATE CYCLASE / RNA CYCLASE / RNA-3'-PHOSPHATE CYCLASE


Mass: 37014.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: RTCA / Plasmid: PET-11D_ECOLI CYCLASE / Cellular location (production host): CYTOPLASM / Gene (production host): RTCA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-DTO / 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL


Mass: 170.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsC-TERMINAL HIS TAG ADDED

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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: 2.84 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.5
Details: THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG 2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
213-15 %mPEG20001reservoir
3200 mMNa citrate1reservoir
4200 mMTris-HCl1reservoir
52 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.96456
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96456 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 50057 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.043 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.268 / % possible all: 83.4
Reflection
*PLUS
Num. measured all: 159690 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 83.4 % / Rmerge(I) obs: 0.268

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMI, CHAIN A

1qmi


Resolution: 2.1→10 Å / SU B: 5.47 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.215
Details: REFINEMENT WAS STARTED WITH XPLOR 3.1, THE HIS TAG OF CHAINS A AND B WERE NOT VISIBLE IN THE ELECTRON DENSITY. THE ELECTRON DENSITY AROUND RESIDUES 94 TO 97 COULD NOT BE MODELLED WITH STANDARD BACKBONE GEOMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2286 5 %RANDOM
Rwork0.204 ---
obs0.207 48203 93.6 %-
Displacement parametersBiso mean: 37.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 35 424 5430
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0560.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.62
X-RAY DIFFRACTIONp_mcangle_it3.83
X-RAY DIFFRACTIONp_scbond_it32
X-RAY DIFFRACTIONp_scangle_it4.63
X-RAY DIFFRACTIONp_plane_restr0.029
X-RAY DIFFRACTIONp_chiral_restr0.1850.15
X-RAY DIFFRACTIONp_singtor_nbd0.1960.3
X-RAY DIFFRACTIONp_multtor_nbd0.2610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1710.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor17.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.120
X-RAY DIFFRACTIONp_special_tor

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