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- PDB-5kpt: PANK3-AMPPNP complex -

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Basic information

Entry
Database: PDB / ID: 5kpt
TitlePANK3-AMPPNP complex
ComponentsPantothenate kinase 3
KeywordsTRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase
Function / homology
Function and homology information


Coenzyme A biosynthesis / vitamin binding / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Nucleotidyltransferase; domain 5 - #510 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / Helix non-globular / Special / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Nucleotidyltransferase; domain 5 - #510 / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / Helix non-globular / Special / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsWhite, S.W. / Yun, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Allosteric Regulation of Mammalian Pantothenate Kinase.
Authors: Subramanian, C. / Yun, M.K. / Yao, J. / Sharma, L.K. / Lee, R.E. / White, S.W. / Jackowski, S. / Rock, C.O.
History
DepositionJul 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Oct 4, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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.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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7184
Polymers42,1261
Non-polymers5933
Water1,22568
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4378
Polymers84,2522
Non-polymers1,1856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6970 Å2
ΔGint-45 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.463, 97.463, 68.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Pantothenate kinase 3 / / hPanK3 / Pantothenic acid kinase 3


Mass: 42125.750 Da / Num. of mol.: 1 / Fragment: UNP resdiues 12-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H999, pantothenate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.642 Å / Num. obs: 16737 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.8 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KPR

5kpr


Resolution: 2.301→39.642 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 833 4.98 %Random selection
Rwork0.1755 ---
obs0.1785 16723 98.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.42 Å2
Refinement stepCycle: LAST / Resolution: 2.301→39.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 36 68 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012735
X-RAY DIFFRACTIONf_angle_d1.0913692
X-RAY DIFFRACTIONf_dihedral_angle_d12.828967
X-RAY DIFFRACTIONf_chiral_restr0.043413
X-RAY DIFFRACTIONf_plane_restr0.004463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.44490.31021310.22232489X-RAY DIFFRACTION95
2.4449-2.63370.2811380.18892651X-RAY DIFFRACTION100
2.6337-2.89860.23171360.17682626X-RAY DIFFRACTION100
2.8986-3.31790.24061400.17412658X-RAY DIFFRACTION100
3.3179-4.17950.22621410.15932683X-RAY DIFFRACTION100
4.1795-39.6420.21671470.17542783X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.60510.3133-1.45811.48240.04152.3910.1035-0.3740.08110.1969-0.11150.1942-0.0910.06290.00670.2231-0.0123-0.0140.21140.00050.1914-21.832122.0074-6.281
27.89911.7536-1.20835.21472.01526.6453-0.1918-0.33040.13070.16040.3076-0.132-0.04610.1446-0.11570.21750.0488-0.04510.3129-0.01510.2992-21.822316.0452-9.6633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A AND RESID 12:369A12 - 369
2X-RAY DIFFRACTION2CHAIN A AND RESID 402:402A402

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