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- PDB-4ff4: N4 mini-vRNAP transcription initiation complex, 4 min after soaki... -

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Basic information

Entry
Database: PDB / ID: 4ff4
TitleN4 mini-vRNAP transcription initiation complex, 4 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 MONOPHOSPHATE / : / PHOSPHATE ION / PYROPHOSPHATE 2- / DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage N4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.026 Å
AuthorsMurakami, K.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 31, 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 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.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)269,56210
Polymers268,4314
Non-polymers1,1316
Water21,5821198
1
A: Virion RNA polymerase
C: Bacteriophage N4 P2 promoter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2527
Polymers134,2162
Non-polymers1,0365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-25 kcal/mol
Surface area46090 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 area4090 Å2
ΔGint-18 kcal/mol
Surface area46720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.398, 111.779, 276.894
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 , 6 types, 1204 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 1198 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
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: 2.03→43.9 Å / Num. obs: 156753 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 %

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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: 2.026→43.87 Å / SU ML: 0.64 / σ(F): 1.36 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 1999 1.28 %Random
Rwork0.1909 ---
obs0.1915 156753 94.09 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.685 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1525 Å2-0 Å20 Å2
2---4.3644 Å2-0 Å2
3---0.2119 Å2
Refinement stepCycle: LAST / Resolution: 2.026→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16908 826 66 1198 18998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618163
X-RAY DIFFRACTIONf_angle_d0.92924754
X-RAY DIFFRACTIONf_dihedral_angle_d15.6976901
X-RAY DIFFRACTIONf_chiral_restr0.0612835
X-RAY DIFFRACTIONf_plane_restr0.0043088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0258-2.07640.37871070.31798287X-RAY DIFFRACTION71
2.0764-2.13260.31751340.294210325X-RAY DIFFRACTION89
2.1326-2.19530.33621360.270910595X-RAY DIFFRACTION91
2.1953-2.26620.32011390.255510692X-RAY DIFFRACTION92
2.2662-2.34720.28531410.240910901X-RAY DIFFRACTION93
2.3472-2.44120.28911420.226811082X-RAY DIFFRACTION95
2.4412-2.55220.26051450.222411155X-RAY DIFFRACTION96
2.5522-2.68680.28091460.216211335X-RAY DIFFRACTION97
2.6868-2.85510.26371480.204511445X-RAY DIFFRACTION98
2.8551-3.07550.22971480.198911466X-RAY DIFFRACTION98
3.0755-3.38490.24721510.190311643X-RAY DIFFRACTION99
3.3849-3.87440.2051520.164211766X-RAY DIFFRACTION99
3.8744-4.88030.1831530.13311852X-RAY DIFFRACTION99
4.8803-43.88010.20031570.161712210X-RAY DIFFRACTION99
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)
10.172-0.09650.14890.80930.16420.9928-0.02-0.0385-0.0162-0.0313-0.01490.0097-0.0111-0.0279-00.12040.0164-0.01930.15840.0240.147921.2495-45.5652400.1867
20.3718-0.04190.1220.20450.06490.2719-0.02010.0391-0.0039-0.02110.0052-0.0496-0.0110.0291-00.1266-0.01790.00830.12650.00270.138614.5015-39.0739362.6855
30.72830.3496-0.08340.5524-0.76750.515-0.09510.0486-0.112-0.14310.0241-0.1982-0.0631-0.0825-0.03550.2555-0.07740.04040.1923-0.00930.37233.1015-11.2081362.8521
40.1618-0.2446-0.05450.6758-0.1962-0.2931-0.1593-0.04810.02730.13070.1145-0.0319-0.2091-0.0422-0.01740.19830.0008-0.00930.1944-0.01510.118914.2042-19.1795390.5645
50.1605-0.1004-0.1499-0.3176-0.23480.85170.00810.0256-0.0091-0.00640.01420.0356-0.2308-0.09050.00420.15290.0049-0.020.1212-0.00470.1149-3.8735-17.5585372.5259
60.0397-0.14410.00010.87480.30610.35480.1859-0.80130.1195-0.4766-0.1194-0.1101-0.53460.25150.0040.2753-0.0812-0.00810.4520.03540.319915.9758-23.7653384.5955
70.20440.0527-0.18020.15410.16060.1601-0.0182-0.18680.07340.02320.0178-0.2394-0.36390.2561-0.00930.4025-0.0421-0.05370.2564-0.01880.251831.2822-24.5306409.3828
80.32980.0049-0.29850.5409-0.33550.77040.0296-0.04210.0235-0.07340.0213-0.0435-0.0385-0.02540.01150.1186-0.01760.03350.12-0.00960.128348.3326-59.5067403.0931
90.2250.0421-0.11740.5102-0.05190.1435-0.00130.01340.0232-0.03210.02550.1030.02570.03780.00050.1519-0.03860.02280.13670.00550.169264.126-64.0751368.1479
101.10780.1940.24910.7450.6130.5174-0.1762-0.03390.1365-0.19780.04770.2743-0.01660.1982-0.0540.2518-0.0862-0.08520.17350.00540.340943.7552-89.9773361.5681
110.0419-0.07590.0630.2178-0.0446-0.1389-0.0844-0.0569-0.06130.00440.04740.05760.05710.0488-0.00620.15590.00170.01160.17730.00970.160956.7821-85.2984392.4835
120.2974-0.0223-0.2680.1036-0.20140.8165-0.0198-0.056-0.0661-0.0936-0.0239-0.06850.13570.1397-00.15240.00870.01360.1937-0.00520.180378.0447-88.6194380.4649
130.01-0.0141-0.0287-0.0011-0.0061-0.0049-0.0174-0.10660.1557-0.22420.5050.37330.3271-0.0640.00020.5323-0.0023-0.09150.6221-0.05470.598555.7437-80.4858387.6486
140.3275-0.1080.1870.0496-0.11050.14020.0204-0.1273-0.1801-0.1070.066-0.02850.3572-0.28180.00860.216-0.0897-0.01210.2019-0.00440.174634.6623-80.0813407.5156
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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