[English] 日本語
Yorodumi
- PDB-9guh: Crystal structure of NtcA from S. elongatus in apo form B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9guh
TitleCrystal structure of NtcA from S. elongatus in apo form B
ComponentsGlobal nitrogen regulator
KeywordsDNA BINDING PROTEIN / DNA binding protein. Transcriptional regulation / NtcA / nitrogen regulation / cyanobacteria
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Transcription regulator, NtcA / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...Transcription regulator, NtcA / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Global nitrogen regulator
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsLlacer, J.L. / Forcada-Nadal, A. / Rubio, V.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116880GB-I00 Spain
Spanish Ministry of Economy and CompetitivenessBFU2017-84264-P Spain
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase.
Authors: Forcada-Nadal, A. / Bibak, S. / Salinas, P. / Contreras, A. / Rubio, V. / Llacer, J.L.
History
DepositionSep 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Global nitrogen regulator


Theoretical massNumber of molelcules
Total (without water)24,8621
Polymers24,8621
Non-polymers00
Water00
1
A: Global nitrogen regulator

A: Global nitrogen regulator


Theoretical massNumber of molelcules
Total (without water)49,7242
Polymers49,7242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area2580 Å2
ΔGint-19 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.385, 96.385, 126.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Global nitrogen regulator


Mass: 24862.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Gene: ntcA, Synpcc7942_0127 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P29283
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: NtcA protein was at 6,1 mg/ml in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate. CRYSTALLIZATION SOLUTION: 0,05 M Tris-HCL ...Details: NtcA protein was at 6,1 mg/ml in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate. CRYSTALLIZATION SOLUTION: 0,05 M Tris-HCL pH8, 2M NaCl, 2% 2-methyl-2,4-pentanediol,10mM MgCl2, 5%DMSO. CRYO PROTECTANT: 27% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.3→83.5 Å / Num. obs: 5530 / % possible obs: 100 % / Redundancy: 6.6 % / Rsym value: 0.136 / Net I/σ(I): 4
Reflection shellResolution: 3.3→3.51 Å / Num. unique obs: 5530 / Rsym value: 0.419

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.33→48.19 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.861 / SU B: 61.645 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27392 247 4.5 %RANDOM
Rwork0.22198 ---
obs0.22441 5253 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å2-0 Å2
2---0.29 Å2-0 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 3.33→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 0 0 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121685
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161615
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6352282
X-RAY DIFFRACTIONr_angle_other_deg0.5061.5463738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.78513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65510295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1254.892863
X-RAY DIFFRACTIONr_mcbond_other5.0854.895863
X-RAY DIFFRACTIONr_mcangle_it7.8687.3321077
X-RAY DIFFRACTIONr_mcangle_other7.8797.3321078
X-RAY DIFFRACTIONr_scbond_it5.6595.184822
X-RAY DIFFRACTIONr_scbond_other5.6565.185823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4547.6471206
X-RAY DIFFRACTIONr_long_range_B_refined11.65494.2836607
X-RAY DIFFRACTIONr_long_range_B_other11.64994.2866607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.33→3.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 16 -
Rwork0.229 365 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 35.325 Å / Origin y: -25.0982 Å / Origin z: -5.9671 Å
111213212223313233
T0.1042 Å20.04 Å2-0.0291 Å2-0.1216 Å2-0.0454 Å2--0.0562 Å2
L1.4733 °20.6147 °2-0.5849 °2-1.0134 °2-1.4121 °2--2.6437 °2
S0.0071 Å °0.0538 Å °0.0871 Å °-0.0738 Å °0.0711 Å °0.1452 Å °-0.0723 Å °-0.3217 Å °-0.0783 Å °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more