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- PDB-4ff3: N4 mini-vRNAP transcription initiation complex, 3 min after soaki... -

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Basic information

Entry
Database: PDB / ID: 4ff3
TitleN4 mini-vRNAP transcription initiation complex, 3 min after soaking GTP, ATP and Mn
Components
  • Bacteriophage N4 P2 promoter
  • Virion RNA polymerase
KeywordsTRANSFERASE/DNA / RNA polymerase / TRANSFERASE-DNA 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 / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain ...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 / 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
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / : / PHOSPHATE ION / DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage N4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsMurakami, K.S. / Basu, R.S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography.
Authors: Basu, R.S. / Murakami, K.S.
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Virion RNA polymerase
C: Bacteriophage N4 P2 promoter
B: Virion RNA polymerase
D: Bacteriophage N4 P2 promoter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,60110
Polymers268,4314
Non-polymers1,1706
Water22,4291245
1
A: Virion RNA polymerase
C: Bacteriophage N4 P2 promoter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2917
Polymers134,2162
Non-polymers1,0755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-32 kcal/mol
Surface area46230 Å2
MethodPISA
2
B: Virion RNA polymerase
D: Bacteriophage N4 P2 promoter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3113
Polymers134,2162
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-17 kcal/mol
Surface area46870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.019, 111.652, 276.145
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: 123193.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage N4 (virus) / Plasmid: PKMK56 / Production host: Escherichia coli (E. coli) / References: UniProt: Q859P9
#2: DNA chain Bacteriophage N4 P2 promoter


Mass: 11022.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Bacteriophage N4 P2 promoter DNA

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Non-polymers , 5 types, 1251 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1245 / 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: 47.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25 % (DROP) 15% (RESERVOIR) PEG 3350 , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.997→42.382 Å / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→42.382 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1999 1.3 %
Rwork0.1821 --
obs0.1825 153225 88.89 %
all-582255 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.574 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0207 Å2-0 Å20 Å2
2---3.6623 Å20 Å2
3---1.6416 Å2
Refinement stepCycle: LAST / Resolution: 1.997→42.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16908 826 67 1245 19046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418163
X-RAY DIFFRACTIONf_angle_d0.86324754
X-RAY DIFFRACTIONf_dihedral_angle_d15.2156900
X-RAY DIFFRACTIONf_chiral_restr0.0572834
X-RAY DIFFRACTIONf_plane_restr0.0043088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9968-2.04680.30111230.2339330X-RAY DIFFRACTION78
2.0468-2.10210.25831260.20979489X-RAY DIFFRACTION79
2.1021-2.1640.24031250.19979512X-RAY DIFFRACTION79
2.164-2.23380.22421290.19369661X-RAY DIFFRACTION80
2.2338-2.31360.26951310.19899929X-RAY DIFFRACTION83
2.3136-2.40630.26731370.203410339X-RAY DIFFRACTION86
2.4063-2.51580.26841410.200710650X-RAY DIFFRACTION88
2.5158-2.64840.251450.206511015X-RAY DIFFRACTION91
2.6484-2.81430.23881490.204711251X-RAY DIFFRACTION93
2.8143-3.03150.21831530.211311551X-RAY DIFFRACTION95
3.0315-3.33650.23121550.198711764X-RAY DIFFRACTION97
3.3365-3.8190.2081600.172312117X-RAY DIFFRACTION99
3.819-4.81050.1641610.139812219X-RAY DIFFRACTION99
4.8105-42.39180.15311640.161512399X-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)
10.6289-0.25770.21681.38190.31171.4981-0.0276-0.0245-0.0055-0.0105-0.02090.0447-0.0794-0.08460.02060.11390.0018-0.01870.14810.02250.119420.9804-45.5484399.1152
20.6728-0.20030.12610.54340.05980.5819-0.00270.0703-0.0138-0.0428-0.0024-0.10510.03270.0840.00750.1089-0.0284-0.00090.1214-0.00840.129214.3992-39.0258361.7475
31.55320.5130.19491.1105-0.60520.7275-0.06220.1798-0.1934-0.23270.0079-0.27490.01460.08660.00540.2454-0.08710.01880.1895-0.00190.320532.9416-11.2481361.9638
40.4396-0.38140.23490.8798-0.30910.234-0.1633-0.09190.04880.21070.1399-0.0614-0.2142-0.0627-0.00650.22730.0041-0.01590.1758-0.03790.134714.0137-19.1897389.5472
50.526-0.2155-0.14850.4335-0.03141.5693-0.008-0.00430.0840.03050.02510.0749-0.3041-0.1160.01460.12650.0048-0.01050.1271-0.00530.1398-3.9913-17.5366371.4972
61.49460.17180.5790.6413-0.50271.98080.039-0.51380.19280.0502-0.0585-0.3161-0.37390.33150.01960.4346-0.1194-0.08770.36390.04870.327315.7846-23.7378383.5883
70.7522-0.2702-0.36811.49060.10472.654-0.0068-0.18810.30160.06580.047-0.3041-0.64460.3014-0.01630.3698-0.0695-0.060.2398-0.02670.244230.9892-24.5251408.2893
80.96880.041-0.46411.2795-0.33481.31590.0065-0.01420.0323-0.15460.0184-0.0959-0.04960.0501-0.03780.0928-0.01310.02830.0902-0.0130.090348.0161-59.4135401.9714
90.4193-0.0252-0.12510.8185-0.12760.51070.01240.00790.0325-0.03780.02720.1488-0.0204-0.0233-0.0250.1306-0.05090.00730.1384-0.0010.160463.771-63.9877367.1251
101.9374-0.1685-0.15141.52930.65630.7812-0.12550.15070.237-0.3983-0.00930.3382-0.11790.03010.0770.2903-0.0772-0.07460.22090.01220.313643.4916-89.8799360.5826
110.3362-0.1152-0.15240.40080.16550.2439-0.1132-0.0747-0.05670.05690.06790.07540.1370.07370.02680.1730.0104-0.00020.17490.03220.162256.4727-85.142391.4302
120.4667-0.0316-0.13450.5468-0.47771.412-0.0234-0.0792-0.1076-0.1095-0.0221-0.13510.23240.21110.0350.12960.01940.00740.1736-0.01050.161877.7116-88.455379.3982
132.1773-0.4684-1.2970.17850.65842.7425-0.0008-0.0047-0.1475-0.23440.34040.42070.227-0.1191-0.28410.4929-0.01270.0070.4695-0.01370.412855.4452-80.3807386.5725
140.568-0.50260.33240.5719-0.0582.2988-0.0034-0.0676-0.2312-0.18140.02330.11910.6176-0.3319-0.02370.3122-0.1034-0.0040.2096-0.00480.221434.4809-80.0396406.4836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:297)
2X-RAY DIFFRACTION2(chain A and resid 298:619)
3X-RAY DIFFRACTION3(chain A and resid 620:762)
4X-RAY DIFFRACTION4(chain A and resid 763:921)
5X-RAY DIFFRACTION5(chain A and resid 922:1100)
6X-RAY DIFFRACTION6(chain C and resid 3:9)
7X-RAY DIFFRACTION7(chain C and resid 10:22)
8X-RAY DIFFRACTION8(chain B and resid 6:298)
9X-RAY DIFFRACTION9(chain B and resid 299:619)
10X-RAY DIFFRACTION10(chain B and resid 620:761)
11X-RAY DIFFRACTION11(chain B and resid 762:934)
12X-RAY DIFFRACTION12(chain B and resid 935:1100)
13X-RAY DIFFRACTION13(chain D and resid 3:9)
14X-RAY DIFFRACTION14(chain D and resid 10:22)

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