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- PDB-2j9d: Structure of GlnK1 with bound effectors indicates regulatory mech... -

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Basic information

Entry
Database: PDB / ID: 2j9d
TitleStructure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake
Components(HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN ...) x 2
KeywordsMEMBRANE TRANSPORT / EM SINGLE PARTICLE / NITROGEN METABOLISM / SIGNALLING / TRANSCRIPTION / HYPOTHETICAL PROTEIN / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol
Similarity search - Function
Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits ...Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Nitrogen regulatory protein GlnK1
Similarity search - Component
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYildiz, O. / Kalthoff, C. / Raunser, S. / Kuehlbrandt, W.
CitationJournal: Embo J. / Year: 2007
Title: Structure of Glnk1 with Bound Effectors Indicates Regulatory Mechanism for Ammonia Uptake.
Authors: Yildiz, O. / Kalthoff, C. / Raunser, S. / Kuhlbrandt, W.
History
DepositionNov 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
B: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
C: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
D: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
E: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
F: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
G: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
H: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
I: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
J: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
K: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
L: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,14023
Polymers159,75412
Non-polymers2,38711
Water12,502694
1
A: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
B: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
C: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4806
Polymers39,9343
Non-polymers5453
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
E: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
F: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3575
Polymers39,9503
Non-polymers4062
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
G: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
H: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
I: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4215
Polymers39,9343
Non-polymers4862
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
J: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
K: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
L: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8837
Polymers39,9343
Non-polymers9494
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.600, 107.030, 134.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN ... , 2 types, 12 molecules ABCDFGHIJKLE

#1: Protein
HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059 / GLNK1


Mass: 13311.469 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) / Strain: AMJFT37 / Plasmid: PET28-D2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60381
#2: Protein HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059 / GLNK1


Mass: 13327.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) / Strain: AMJFT37 / Plasmid: PET28-D2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60381

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Non-polymers , 5 types, 705 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 80980 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.06 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J9C

2j9c


Resolution: 2.1→19.78 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.657 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4050 5 %RANDOM
Rwork0.207 ---
obs0.21 76930 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9994 0 152 694 10840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210214
X-RAY DIFFRACTIONr_bond_other_d0.0020.027242
X-RAY DIFFRACTIONr_angle_refined_deg1.4462.02313719
X-RAY DIFFRACTIONr_angle_other_deg0.944317811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95451286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32824.695394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.209152063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2931587
X-RAY DIFFRACTIONr_chiral_restr0.0790.21634
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210924
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021766
X-RAY DIFFRACTIONr_nbd_refined0.2120.21934
X-RAY DIFFRACTIONr_nbd_other0.2070.27778
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24817
X-RAY DIFFRACTIONr_nbtor_other0.0850.26107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2694
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.27938370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.673510439
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.47764159
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.83573280
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 291
Rwork0.239 5511

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