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- PDB-4rnp: BACTERIOPHAGE T7 RNA POLYMERASE, HIGH SALT CRYSTAL FORM, LOW TEMP... -

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Basic information

Entry
Database: PDB / ID: 4rnp
TitleBACTERIOPHAGE T7 RNA POLYMERASE, HIGH SALT CRYSTAL FORM, LOW TEMPERATURE DATA, ALPHA-CARBONS ONLY
ComponentsRNA POLYMERASE
KeywordsNUCLEOTIDYLTRANSFERASE / RNA POLYMERASE / TRANSCRIPTION
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / DNA-templated transcription / DNA binding
Similarity search - Function
DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 3 Å
AuthorsLiu, Z.J. / Sousa, R. / Rose, J.P. / Wang, B.C.
Citation
Journal: Nature / Year: 1993
Title: Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution.
Authors: Sousa, R. / Chung, Y.J. / Rose, J.P. / Wang, B.C.
#1: Journal: J.Cryst.Growth / Year: 1991
Title: Preparation of Crystals of T7 RNA Polymerase Suitable for High-Resolution X-Ray Structure Analysis
Authors: Sousa, R. / Lafer, E.M. / Wang, B.C.
#2: Journal: Methods (San Diego) / Year: 1990
Title: The Use of Glycerol in the Crystallization of T7 RNA Polymerase: Implications for the Use of Co-Solvents in Protein Crystallization
Authors: Sousa, R. / Lafer, E.M.
#3: Journal: Proteins / Year: 1989
Title: Single Crystals of Bacteriophage T7 RNA Polymerase
Authors: Sousa, R. / Rose, J.P. / Chung, Y.J. / Lafer, E.M. / Wang, B.C.
#4: Journal: J.Mol.Biol. / Year: 1984
Title: Nucleotide Sequence of the Gene for Bacteriophage T7 RNA Polymerase
Authors: Moffatt, B.A. / Dunn, J.J. / Studier, F.W.
History
DepositionSep 11, 1997Processing site: BNL
SupersessionDec 3, 1997ID: 3RNP
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA POLYMERASE
B: RNA POLYMERASE
C: RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)296,9533
Polymers296,9533
Non-polymers00
Water00
1
A: RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)98,9841
Polymers98,9841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)98,9841
Polymers98,9841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)98,9841
Polymers98,9841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.267, 137.681, 122.566
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS THREE MOLECULES DENOTED AS CHAINS 'A', 'B', AND 'C' IN THIS ENTRY. THE THREE CHAIN ARE RELATED BY LOCAL 3(1) SYMMETRY.

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Components

#1: Protein RNA POLYMERASE / T7 RNAP / DNA-DIRECTED RNA POLYMERASE / Coordinate model: Cα atoms only


Mass: 98984.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HIGH SALT FORM, LOW TEMPERATURE DATA / Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Cell line: 293 / Gene: T7 RNAP / Plasmid: T7 / Gene (production host): T7 RNAP / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P00573, DNA-directed RNA polymerase

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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: 3.38 Å3/Da / Density % sol: 64 %
Crystal grow
*PLUS

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Data collection

DiffractionMean temperature: 81 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 1996 / Details: YALE/MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 88576 / % possible obs: 77.52 % / Observed criterion σ(I): 2 / Redundancy: 4.11 % / Rsym value: 0.138

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Processing

Software
NameClassification
ISIRphasing
PHASESphasing
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MIRAS / Highest resolution: 3 Å
Details: UNREFINED ALPHA CARBON MODEL THE COORDINATES PRESENTED IN THIS ENTRY ARE UNREFINED ALPHA CARBON COORDINATES OBTAINED FROM HIGHER RESOLUTION LOW TEMPERATURE DATA. THE REFINEMENT IS IN ...Details: UNREFINED ALPHA CARBON MODEL THE COORDINATES PRESENTED IN THIS ENTRY ARE UNREFINED ALPHA CARBON COORDINATES OBTAINED FROM HIGHER RESOLUTION LOW TEMPERATURE DATA. THE REFINEMENT IS IN PROGRESS. THE FULL COORDINATE SET WILL BE DEPOSITED ONCE THE REFINEMENT IS COMPLETE. THERE ARE 10 REGIONS OF UNDEFINED DENSITY IN EACH CHAIN. THESE REGIONS ARE ALL LOCATED ON THE MOLECULAR SURFACE. REGION 1 RESIDUES 1 - 6 REGION 2 RESIDUES 57 - 70 REGION 3 RESIDUES 164 - 179 REGION 4 RESIDUES 232 - 240 REGION 5 RESIDUES 346 - 348 REGION 6 RESIDUES 495 - 499 REGION 7 RESIDUES 587 - 610 REGION 8 RESIDUES 636 - 645 REGION 9 RESIDUES 709 - 720 REGION 10 RESIDUES 751 - 754 IN TOTAL, THERE ARE 780 (88.4%) RESIDUES ASSIGNED IN ELECTRON DENSITY MAP AND 103 (11.6%) RESIDUES ARE MISSING.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 0 0 2340

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