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- PDB-3q24: X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter t... -

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Basic information

Entry
Database: PDB / ID: 3q24
TitleX-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with pppGpG and pyrophosphate: product complex
Components
  • DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
  • Virion RNA polymerase
KeywordsTRANSFERASE/DNA/RNA / PROTEIN-DNA COMPLEX / TWO-METAL CATALYSIS / DE NOVO TRANSCRIPTION INITIATION / NUCLEOTIDYLTRANSFERASE / INITIATION COMPLEX / DNA-HAIRPIN / VIRION RNA POLYMERASE / TRANSFERASE-DNA-RNA COMPLEX
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / virion component / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #110 / Alpha-Beta Plaits - #2440 / Transcription Regulator spoIIAA - #220 / Helix Hairpins - #1360 / Helix Hairpins - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1860 / : / : / : / : ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #110 / Alpha-Beta Plaits - #2440 / Transcription Regulator spoIIAA - #220 / Helix Hairpins - #1360 / Helix Hairpins - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1860 / : / : / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain / Virion DNA-directed RNA polymerase domain / Bacteriophage N4 RNA polymerase, helical domain / Transcription Regulator spoIIAA / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage N4 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGleghorn, M.L. / Murakami, K.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
Authors: Gleghorn, M.L. / Davydova, E.K. / Basu, R. / Rothman-Denes, L.B. / Murakami, K.S.
History
DepositionDec 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / ndb_struct_conf_na / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion RNA polymerase
B: Virion RNA polymerase
C: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
D: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,51910
Polymers268,0874
Non-polymers1,4326
Water43,2182399
1
A: Virion RNA polymerase
C: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2036
Polymers134,0432
Non-polymers1,1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-10 kcal/mol
Surface area46750 Å2
MethodPISA
2
B: Virion RNA polymerase
D: DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3164
Polymers134,0432
Non-polymers2732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-8 kcal/mol
Surface area47180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.459, 111.790, 277.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein Virion RNA polymerase


Mass: 123036.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage N4 (virus) / Gene: gp50 / Plasmid: PKMK56 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q859P9, DNA-directed RNA polymerase
#2: DNA chain DNA (5'-D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3')


Mass: 11007.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 2405 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O4P
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 294 K / Method: hanging drop / pH: 8
Details: 0.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25% (DROP) 21.5-22% (RESERVOIR) PEG 3350, pH 8.0, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS-HCL11
2DIBASIC AMMONIUM CITRATE11
3AMMONIUM DIHYDROGEN MONOPHOSPHATE11
4PEG 335011
5TRIS-HCL12
6DIBASIC AMMONIUM CITRATE12
7AMMONIUM DIHYDROGEN MONOPHOSPHATE12
8PEG 335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.959997
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2006
RadiationMonochromator: Silicon(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959997 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 233493 / Num. obs: 233493 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.728 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→41.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.791 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 11698 5 %RANDOM
Rwork0.201 ---
all0.202 233362 --
obs0.202 233362 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.81→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16897 881 83 2399 20260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02218231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0962.04224862
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18752187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06225.761769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.905153119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.761582
X-RAY DIFFRACTIONr_chiral_restr0.0750.22846
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213301
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.29159
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.212654
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7261.511217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94217537
X-RAY DIFFRACTIONr_scbond_it1.40138174
X-RAY DIFFRACTIONr_scangle_it2.1524.57325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 799 -
Rwork0.298 14183 -
obs--86.58 %

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