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- PDB-5d1f: Crystal structure of maize PDRP bound with AMP and Hg2+ -

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Basic information

Entry
Database: PDB / ID: 5d1f
TitleCrystal structure of maize PDRP bound with AMP and Hg2+
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: 3.4 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 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Mar 12, 2025Group: Database references / Refinement description / Category: pdbx_database_related / software
Item: _pdbx_database_related.content_type / _software.classification

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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)45,2994
Polymers44,7271
Non-polymers5723
Water28816
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)90,5998
Polymers89,4552
Non-polymers1,1446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area9930 Å2
ΔGint-124 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.514, 175.514, 175.514
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-615-

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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 16 / 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: 5.04 Å3/Da / Density % sol: 75.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: peg, dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 13309 / Num. obs: 13309 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 217.2 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/av σ(I): 55.5 / Net I/σ(I): 55.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 3.4→48.68 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.884 / SU B: 15.532 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.523 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24273 661 5 %RANDOM
Rwork0.22305 ---
obs0.22404 12469 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.392 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.4→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 25 16 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192038
X-RAY DIFFRACTIONr_bond_other_d0.0020.021831
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9682795
X-RAY DIFFRACTIONr_angle_other_deg0.95734185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0515271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.08925.26376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.20115276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.212156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212358
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
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_it2.9435.0461093
X-RAY DIFFRACTIONr_mcbond_other2.9375.0441092
X-RAY DIFFRACTIONr_mcangle_it5.1747.5411361
X-RAY DIFFRACTIONr_mcangle_other5.1757.5431362
X-RAY DIFFRACTIONr_scbond_it2.9215.09943
X-RAY DIFFRACTIONr_scbond_other2.925.09944
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9277.5391434
X-RAY DIFFRACTIONr_long_range_B_refined8.74839.552309
X-RAY DIFFRACTIONr_long_range_B_other8.74839.5652309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 38 -
Rwork0.382 834 -
obs--93.26 %

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