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- PDB-3o5t: Structure of DraG-GlnZ complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3o5t
TitleStructure of DraG-GlnZ complex with ADP
Components
  • Dinitrogenase reductase activacting glicohydrolase
  • PII-like protein Pz
KeywordsHYDROLASE/TRANSCRIPTION / ADP binding / HYDROLASE-TRANSCRIPTION complex
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / regulation of nitrogen utilization / metabolic process / enzyme regulator activity / ATP binding / metal ion binding
Similarity search - Function
ADP-ribosyl-dinitrogen reductase hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / Nitrogen regulatory protein P-II, urydylation site / ADP-ribosylation/Crystallin J1 superfamily / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. ...ADP-ribosyl-dinitrogen reductase hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / Nitrogen regulatory protein P-II, urydylation site / ADP-ribosylation/Crystallin J1 superfamily / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADP-ribosyl-[dinitrogen reductase] hydrolase / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRajendran, C. / Li, X.-D. / Winkler, F.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction
Authors: Rajendran, C. / Gerhardt, E.C.M. / Bjelic, S. / Gasperina, A. / Scarduelli, M. / Pedrosa, F.O. / Chubatsu, L.S. / Merrick, M. / Souza, E.M. / Winkler, F.K. / Huergo, L.F. / Li, X.-D.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: Dinitrogenase reductase activacting glicohydrolase
B: PII-like protein Pz
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2065
Polymers44,7302
Non-polymers4763
Water7,080393
1
A: Dinitrogenase reductase activacting glicohydrolase
B: PII-like protein Pz
hetero molecules

A: Dinitrogenase reductase activacting glicohydrolase
B: PII-like protein Pz
hetero molecules

A: Dinitrogenase reductase activacting glicohydrolase
B: PII-like protein Pz
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,61715
Polymers134,1906
Non-polymers1,4279
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)115.654, 115.654, 105.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-199-

HOH

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Components

#1: Protein Dinitrogenase reductase activacting glicohydrolase


Mass: 32442.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Strain: FP2 / Gene: draG / Plasmid: pLHPET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: A7XNI2, ADP-ribosyl-[dinitrogen reductase] hydrolase
#2: Protein PII-like protein Pz / PZ protein


Mass: 12287.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Strain: FP2 / Gene: glnZ / Plasmid: PMSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P70731
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG 8000, 0.2M Nacl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2010
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→70 Å / Num. all: 80171 / Num. obs: 31022 / Redundancy: 2.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 13.75
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.205 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
REFMAC5.5.0072refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MHY and 3G9D

3mhy

3g9d


Resolution: 2.09→70 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.164 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19108 1551 5 %RANDOM
Rwork0.15113 ---
obs0.15315 29470 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.288 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.09→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 29 393 3449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223107
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9614208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3565392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47523.431137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1411526
X-RAY DIFFRACTIONr_chiral_restr0.1380.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212324
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1111.51945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95323107
X-RAY DIFFRACTIONr_scbond_it3.55331162
X-RAY DIFFRACTIONr_scangle_it5.4514.51101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.089→2.143 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 110 -
Rwork0.177 2105 -
obs--100 %

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