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- PDB-5kq8: PANK3-AMPPN complex -

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Basic information

Entry
Database: PDB / ID: 5kq8
TitlePANK3-AMPPN 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
AMP PHOSPHORAMIDATE / Pantothenate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6384
Polymers42,1261
Non-polymers5133
Water97354
1
A: Pantothenate kinase 3
hetero molecules

A: Pantothenate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2778
Polymers84,2522
Non-polymers1,0256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area7300 Å2
ΔGint-51 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.477, 98.477, 68.495
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 residues 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-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 54 / 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: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.642 Å / Num. obs: 26151 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 2 / CC1/2: 0.749 / % possible all: 100

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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: 2.002→42.642 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2185 1313 5.02 %
Rwork0.1808 --
obs0.1827 26133 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→42.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 32 54 2803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082810
X-RAY DIFFRACTIONf_angle_d1.0343810
X-RAY DIFFRACTIONf_dihedral_angle_d12.031991
X-RAY DIFFRACTIONf_chiral_restr0.043423
X-RAY DIFFRACTIONf_plane_restr0.004482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0017-2.08180.25581410.22252704X-RAY DIFFRACTION99
2.0818-2.17660.25781480.2112706X-RAY DIFFRACTION100
2.1766-2.29130.23921460.20072747X-RAY DIFFRACTION100
2.2913-2.43490.22181450.18992726X-RAY DIFFRACTION100
2.4349-2.62280.23881420.18542754X-RAY DIFFRACTION100
2.6228-2.88670.231460.18562759X-RAY DIFFRACTION100
2.8867-3.30430.23661450.18692761X-RAY DIFFRACTION100
3.3043-4.16250.18921470.17192784X-RAY DIFFRACTION100
4.1625-42.65140.21411530.17122879X-RAY DIFFRACTION99
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)
12.83870.52071.41961.99680.09222.2640.1639-0.4975-0.04180.2316-0.1951-0.15830.1248-0.16980.00980.2497-0.03890.01230.26540.00160.19422.154-22.0061-6.0423
23.45480.2458-0.99430.7198-0.57061.49370.0108-0.14070.16990.06580.11340.0372-0.0298-0.1495-0.07480.3229-0.0341-0.02790.3703-0.03440.423920.9761-15.7454-8.9591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:369 )A11 - 369
2X-RAY DIFFRACTION2( CHAIN A AND RESID 401:401 )A401

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