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- PDB-5d0n: Crystal structure of maize PDRP bound with AMP -

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Basic information

Entry
Database: PDB / ID: 5d0n
TitleCrystal structure of maize PDRP bound with AMP
ComponentsPyruvate, phosphate dikinase regulatory protein, chloroplastic
KeywordsTRANSFERASE / PDRP / reversible phosphorylation / C4 photosynthesis / ADP-dependent protein kinase/Pi-dependent protein phosphatase
Function / homology
Function and homology information


[pyruvate, phosphate dikinase] kinase / [pyruvate, phosphate dikinase]-phosphate phosphotransferase / phosphotransferase activity, phosphate group as acceptor / chloroplast stroma / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Bifunctional kinase-pyrophosphorylase / Pyruvate Pi dikinase regulator, chloroplast / Putative pyruvate, phosphate dikinase regulatory protein / Kinase/pyrophosphorylase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Pyruvate, phosphate dikinase regulatory protein, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsJiang, L. / Chen, Z.
CitationJournal: Plant Physiol. / Year: 2016
Title: Structural Basis of Reversible Phosphorylation by Maize Pyruvate Orthophosphate Dikinase Regulatory Protein
Authors: Jiang, L. / Chen, Y.B. / Zheng, J. / Chen, Z. / Liu, Y. / Tao, Y. / Wu, W. / Chen, Z. / Wang, B.C.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Data collection
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate, phosphate dikinase regulatory protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0993
Polymers44,7271
Non-polymers3722
Water57632
1
A: Pyruvate, phosphate dikinase regulatory protein, chloroplastic
hetero molecules

A: Pyruvate, phosphate dikinase regulatory protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1986
Polymers89,4552
Non-polymers7434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area9970 Å2
ΔGint-76 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.342, 175.342, 175.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-628-

HOH

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Components

#1: Protein Pyruvate, phosphate dikinase regulatory protein, chloroplastic / Bifunctional dikinase regulatory protein / BFRP / Pyruvate / Pi dikinase regulatory protein / PPDK ...Bifunctional dikinase regulatory protein / BFRP / Pyruvate / Pi dikinase regulatory protein / PPDK regulatory protein


Mass: 44727.297 Da / Num. of mol.: 1 / Fragment: UNP residues 38-426
Mutation: A106V, F238S, V266A, F271L, A310D, G335A, V371A, W375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: PDRP1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q195N6, [pyruvate, phosphate dikinase] kinase, [pyruvate, phosphate dikinase]-phosphate phosphotransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.02 Å3/Da / Density % sol: 75.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG, Bicine and 2% Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2014 / Details: Data is collected at SSRF beamline BL18U
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 15812 / Num. obs: 15812 / % possible obs: 100 % / Redundancy: 54.1 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 59.2
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 49.6 % / Rmerge(I) obs: 0.536 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.624 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23494 785 5 %RANDOM
Rwork0.21974 ---
obs0.2205 14922 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.346 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 24 32 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192095
X-RAY DIFFRACTIONr_bond_other_d0.0020.021939
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9712860
X-RAY DIFFRACTIONr_angle_other_deg0.95934453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.22825.36682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97515317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.836157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02441
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_it3.1645.8721093
X-RAY DIFFRACTIONr_mcbond_other3.1575.8691092
X-RAY DIFFRACTIONr_mcangle_it5.5628.7781361
X-RAY DIFFRACTIONr_mcangle_other5.5638.7811362
X-RAY DIFFRACTIONr_scbond_it2.5986.0641000
X-RAY DIFFRACTIONr_scbond_other2.5966.0641001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5838.9561499
X-RAY DIFFRACTIONr_long_range_B_refined8.85246.5242373
X-RAY DIFFRACTIONr_long_range_B_other8.85246.5352372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.201→3.284 Å
RfactorNum. reflection% reflection
Rfree0.397 56 -
Rwork0.35 980 -
obs--93.25 %

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