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- PDB-5ovo: Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense -

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Basic information

Entry
Database: PDB / ID: 5ovo
TitleStructure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense
Components
  • ADP-ribosyl-(Dinitrogen reductase) hydrolase
  • Nitrogen regulatory protein P-II 1
KeywordsMETAL BINDING PROTEIN / Glycohydrolase
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
ADP-ribosyl-dinitrogen reductase hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / Nitrogen regulatory protein PII, conserved site ...ADP-ribosyl-dinitrogen reductase hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / 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 / 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 / Resolution: 1.55 Å
AuthorsBerthold, C.L. / Hogbom, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense
Authors: Berthold, C.L. / Hogbom, M.
History
DepositionAug 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosyl-(Dinitrogen reductase) hydrolase
B: Nitrogen regulatory protein P-II 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2027
Polymers43,2442
Non-polymers9585
Water9,134507
1
A: ADP-ribosyl-(Dinitrogen reductase) hydrolase
B: Nitrogen regulatory protein P-II 1
hetero molecules

A: ADP-ribosyl-(Dinitrogen reductase) hydrolase
B: Nitrogen regulatory protein P-II 1
hetero molecules

A: ADP-ribosyl-(Dinitrogen reductase) hydrolase
B: Nitrogen regulatory protein P-II 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,60721
Polymers129,7336
Non-polymers2,87415
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17720 Å2
ΔGint-158 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.740, 116.740, 105.616
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-434-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ADP-ribosyl-(Dinitrogen reductase) hydrolase / 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) / Gene: draG, AMK58_04675 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XNI2
#2: Protein Nitrogen regulatory protein P-II 1 / PII-like protein Pz / PZ protein / Transcriptional regulator


Mass: 10801.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: glnZ, ABAZ39_13575, AMK58_13670 / Production host: Escherichia coli (E. coli) / References: UniProt: P70731

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Non-polymers , 4 types, 512 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 35 % (v/v) glycerol ethoxylate, 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.588
11K, H, -L20.412
ReflectionResolution: 1.55→46.8 Å / Num. obs: 77898 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.05 / Net I/σ(I): 10.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.55→45.6 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.703 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.012 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16453 3881 5 %RANDOM
Rwork0.14404 ---
obs0.14505 74016 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.895 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å20 Å2
2---3.42 Å20 Å2
3---6.85 Å2
Refinement stepCycle: 1 / Resolution: 1.55→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 57 507 3583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193192
X-RAY DIFFRACTIONr_bond_other_d0.0010.023062
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.9744342
X-RAY DIFFRACTIONr_angle_other_deg2.54737026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60123.542144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9415539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9371527
X-RAY DIFFRACTIONr_chiral_restr0.1810.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023625
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02736
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_it1.3131.2441591
X-RAY DIFFRACTIONr_mcbond_other1.311.2441590
X-RAY DIFFRACTIONr_mcangle_it1.6521.871988
X-RAY DIFFRACTIONr_mcangle_other1.6521.871989
X-RAY DIFFRACTIONr_scbond_it1.9831.4561601
X-RAY DIFFRACTIONr_scbond_other1.9821.4561602
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6252.1192346
X-RAY DIFFRACTIONr_long_range_B_refined4.84212.2054206
X-RAY DIFFRACTIONr_long_range_B_other4.44811.0643926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 231 -
Rwork0.371 5536 -
obs--99.86 %

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