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- PDB-1aro: T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1aro
TitleT7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME
Components
  • T7 LYSOZYME
  • T7 RNA POLYMERASE
KeywordsCOMPLEX (POLYMERASE/HYDROLASE) / TRANSCRIPTION / DNA-DIRECTED RNA POLYMERASE / HYDROLASE / GLYCOSIDASE / COMPLEX (POLYMERASE-HYDROLASE) / COMPLEX (POLYMERASE-HYDROLASE) complex
Function / homology
Function and homology information


DNA-templated viral transcription / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / negative regulation of viral transcription / viral release from host cell by cytolysis / peptidoglycan catabolic process / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / host cell cytoplasm ...DNA-templated viral transcription / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / negative regulation of viral transcription / viral release from host cell by cytolysis / peptidoglycan catabolic process / DNA-directed RNA polymerase complex / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / host cell cytoplasm / defense response to bacterium / DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
Endolysin T7 type / Helix Hairpins - #260 / Helix Hairpins - #280 / T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / DNA-directed RNA polymerase, helix hairpin domain superfamily / Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / DNA-directed RNA polymerase, N-terminal ...Endolysin T7 type / Helix Hairpins - #260 / Helix Hairpins - #280 / T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / DNA-directed RNA polymerase, helix hairpin domain superfamily / Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / 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. / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Helix Hairpins / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / T7 RNA polymerase / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsSteitz, T. / Jeruzalmi, D.
CitationJournal: EMBO J. / Year: 1998
Title: Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
Authors: Jeruzalmi, D. / Steitz, T.A.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: T7 RNA POLYMERASE
L: T7 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3479
Polymers115,9432
Non-polymers1,4047
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.385, 95.612, 63.582
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein T7 RNA POLYMERASE


Mass: 98936.039 Da / Num. of mol.: 1 / Mutation: C347S, C723S, C839S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: T7 / Plasmid: T7 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase
#2: Protein T7 LYSOZYME / N-ACETYLMURAMOYL-L-ALANINE AMIDASE


Mass: 17007.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: T7 / Plasmid: T7 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P00806, N-acetylmuramoyl-L-alanine amidase
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 69 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion, sitting drop / Details: Jeruzalmi, D., (1997) J. Mol. Biol., 274, 748.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
22.5 mMTris-HCl1drop
35 mMpotassium phosphate1drop
460 mM1dropNaCl
525 mM1dropMgCl2
612-15 %sarcosine1drop
71 mMdithiothreitol1drop
81 mMNa3 EDTA1drop
90.05 %(v/v)beta-hexylglucoside1drop
100.02 %1dropNaN3
11water1reservoirdeionized, 0.500ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1993 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 38310 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13.37
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Rsym value: 0.44 / % possible all: 76.8

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Processing

Software
NameClassification
CNSrefinement
DEMON-ANGELmodel building
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
DEMON-ANGELphasing
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.309 --
Rwork0.262 --
obs0.262 38310 93.9 %
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7599 0 6 0 7605
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8

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