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- PDB-3m0e: Crystal structure of the ATP-bound state of Walker B mutant of Nt... -

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Basic information

Entry
Database: PDB / ID: 3m0e
TitleCrystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain
ComponentsTranscriptional regulator (NtrC family)
KeywordsTRANSCRIPTION / AAA+ ATPase domain / GAFTGA loop / Arginine finger / sigma54 activator / bacterial enhancer binding protein / bacterial transcription / two-component signal transduction / ATP-binding / DNA-binding / Nucleotide-binding / Transcription regulation / molecular motor
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Transcriptional regulator (NtrC family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsChen, B. / Sysoeva, T.A. / Chowdhury, S. / Rusu, M. / Birmanns, S. / Guo, L. / Hanson, J. / Yang, H. / Nixon, B.T.
CitationJournal: Structure / Year: 2010
Title: Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase.
Authors: Chen, B. / Sysoeva, T.A. / Chowdhury, S. / Guo, L. / De Carlo, S. / Hanson, J.A. / Yang, H. / Nixon, B.T.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Oct 13, 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_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.ptnr2_auth_asym_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.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.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
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator (NtrC family)
B: Transcriptional regulator (NtrC family)
C: Transcriptional regulator (NtrC family)
D: Transcriptional regulator (NtrC family)
E: Transcriptional regulator (NtrC family)
F: Transcriptional regulator (NtrC family)
G: Transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,72521
Polymers213,0057
Non-polymers3,72014
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27430 Å2
ΔGint-106 kcal/mol
Surface area68270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)251.209, 242.586, 40.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 138:214 OR RESSEQ 219:384 )
211CHAIN B AND (RESSEQ 138:214 OR RESSEQ 219:384 )
311CHAIN C AND (RESSEQ 138:214 OR RESSEQ 219:384 )
411CHAIN D AND (RESSEQ 138:214 OR RESSEQ 219:384 )
511CHAIN E AND (RESSEQ 138:214 OR RESSEQ 219:384 )
611CHAIN F AND (RESSEQ 138:214 OR RESSEQ 219:384 )
711CHAIN G AND (RESSEQ 138:214 OR RESSEQ 219:384 )

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
Transcriptional regulator (NtrC family)


Mass: 30429.215 Da / Num. of mol.: 7 / Fragment: ATP-ase domain / Mutation: E239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1117, ntrC1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O67198, EC: 3.6.1.3
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M SODIUM CITRATE, 0.01 M FECL3, 0-5% (V/V) JEFFAMINE M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2007 / Details: mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.63→47.637 Å / Num. all: 75935 / Num. obs: 75935 / % possible obs: 99.7 % / Redundancy: 0.0785 % / Biso Wilson estimate: 69.69 Å2 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 4.78 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 83.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
MrBUMPphasing
ELVESrefinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NY6 (RESIDUES 140-380 OF E CHAIN OF NTRC1)

1ny6


Resolution: 2.63→47.637 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 24.89 / Stereochemistry target values: ML
Details: CNS_Solve 1.2 and Coot were also used in refinement.
RfactorNum. reflection% reflection
Rfree0.2407 7580 9.98 %
Rwork0.2055 --
obs0.2091 75935 99.95 %
all-75935 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.117 Å2 / ksol: 0.322 e/Å3
Refinement stepCycle: LAST / Resolution: 2.63→47.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13825 0 224 391 14440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114294
X-RAY DIFFRACTIONf_angle_d1.3419229
X-RAY DIFFRACTIONf_dihedral_angle_d17.1485453
X-RAY DIFFRACTIONf_chiral_restr0.0932114
X-RAY DIFFRACTIONf_plane_restr0.0042415
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1948X-RAY DIFFRACTIONPOSITIONAL
12B1948X-RAY DIFFRACTIONPOSITIONAL0.052
13C1948X-RAY DIFFRACTIONPOSITIONAL0.051
14D1948X-RAY DIFFRACTIONPOSITIONAL0.048
15E1948X-RAY DIFFRACTIONPOSITIONAL0.04
16F1948X-RAY DIFFRACTIONPOSITIONAL0.049
17G1948X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.65990.38722370.30992264X-RAY DIFFRACTION100
2.6599-2.69120.33562530.29972261X-RAY DIFFRACTION100
2.6912-2.7240.35192390.29532273X-RAY DIFFRACTION100
2.724-2.75850.36332370.29462205X-RAY DIFFRACTION100
2.7585-2.79480.33522430.27382212X-RAY DIFFRACTION100
2.7948-2.8330.32772440.26942237X-RAY DIFFRACTION100
2.833-2.87350.3012540.26522277X-RAY DIFFRACTION100
2.8735-2.91640.34662410.27872284X-RAY DIFFRACTION100
2.9164-2.9620.33422550.24912194X-RAY DIFFRACTION100
2.962-3.01050.27612370.24222220X-RAY DIFFRACTION100
3.0105-3.06240.28272590.24622250X-RAY DIFFRACTION100
3.0624-3.11810.30142510.24352323X-RAY DIFFRACTION100
3.1181-3.17810.28392400.22442203X-RAY DIFFRACTION100
3.1781-3.24290.292470.22662236X-RAY DIFFRACTION100
3.2429-3.31340.27822520.21612275X-RAY DIFFRACTION100
3.3134-3.39050.25952610.21032309X-RAY DIFFRACTION100
3.3905-3.47520.21932520.19742192X-RAY DIFFRACTION100
3.4752-3.56920.22792540.18422252X-RAY DIFFRACTION100
3.5692-3.67410.21782640.17912312X-RAY DIFFRACTION100
3.6741-3.79270.23612370.18852227X-RAY DIFFRACTION100
3.7927-3.92820.19892690.15882261X-RAY DIFFRACTION100
3.9282-4.08540.19162310.17122355X-RAY DIFFRACTION100
4.0854-4.27120.19752640.15992223X-RAY DIFFRACTION100
4.2712-4.49620.16892570.14842341X-RAY DIFFRACTION100
4.4962-4.77770.20872580.14452242X-RAY DIFFRACTION100
4.7777-5.14620.16922590.14472362X-RAY DIFFRACTION100
5.1462-5.66330.18132810.152287X-RAY DIFFRACTION100
5.6633-6.48110.20012550.16562347X-RAY DIFFRACTION100
6.4811-8.15880.1712730.1562414X-RAY DIFFRACTION100
8.1588-47.64470.17592760.172517X-RAY DIFFRACTION99

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