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- PDB-3bmb: Crystal structure of a new RNA polymerase interacting protein -

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Basic information

Entry
Database: PDB / ID: 3bmb
TitleCrystal structure of a new RNA polymerase interacting protein
ComponentsRegulator of nucleoside diphosphate kinase
KeywordsRNA BINDING PROTEIN / RNA polymerase / elongation factor / anti-Gre factor
Function / homology
Function and homology information


DNA-templated transcription elongation / RNA polymerase binding / regulation of DNA-templated transcription elongation / DNA binding
Similarity search - Function
Regulator of nucleoside diphosphate kinase / Regulator of nucleoside diphosphate kinase, N-terminal domain / Rnk N-terminus / GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / GTP Cyclohydrolase I; Chain A, domain 1 ...Regulator of nucleoside diphosphate kinase / Regulator of nucleoside diphosphate kinase, N-terminal domain / Rnk N-terminus / GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / GTP Cyclohydrolase I; Chain A, domain 1 / Chitinase A; domain 3 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Regulator of nucleoside diphosphate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.91 Å
AuthorsDarst, S.A. / Lamour, V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein.
Authors: Lamour, V. / Rutherford, S.T. / Kuznedelov, K. / Ramagopal, U.A. / Gourse, R.L. / Severinov, K. / Darst, S.A.
History
DepositionDec 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Regulator of nucleoside diphosphate kinase
B: Regulator of nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,91214
Polymers29,8802
Non-polymers1,03212
Water5,008278
1
A: Regulator of nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4567
Polymers14,9401
Non-polymers5166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulator of nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4567
Polymers14,9401
Non-polymers5166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.500, 133.400, 66.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Regulator of nucleoside diphosphate kinase


Mass: 14940.013 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rnk / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFW4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50mM Mes, 10mM MgCl2, 1.5M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.74326 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2005 / Details: Double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74326 Å / Relative weight: 1
ReflectionResolution: 1.91→20 Å / Num. obs: 22457 / % possible obs: 98.8 % / Redundancy: 17.2 % / Rsym value: 0.062 / Net I/σ(I): 53.3
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 16.5 % / Mean I/σ(I) obs: 13.7 / Num. unique all: 4432 / Rsym value: 0.233 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
XPREPdata reduction
SOLVEphasing
RefinementResolution: 1.91→19.86 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2211 9.3 %RANDOM
Rwork0.213 ---
all-23688 --
obs-22309 94.2 %-
Solvent computationBsol: 58.462 Å2
Displacement parametersBiso mean: 31.021 Å2
Baniso -1Baniso -2Baniso -3
1--8.1 Å20 Å20 Å2
2--5.728 Å20 Å2
3---2.372 Å2
Refinement stepCycle: LAST / Resolution: 1.91→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 52 278 2404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.402
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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