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- PDB-1esm: STRUCTURAL BASIS FOR THE FEEDBACK REGULATION OF ESCHERICHIA COLI ... -

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Basic information

Entry
Database: PDB / ID: 1esm
TitleSTRUCTURAL BASIS FOR THE FEEDBACK REGULATION OF ESCHERICHIA COLI PANTOTHENATE KINASE BY COENZYME A
ComponentsPANTOTHENATE KINASE
KeywordsTRANSFERASE / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


pantetheine kinase activity / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Pantothenate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsYun, M. / Park, C.G. / Kim, J.Y. / Rock, C.O. / Jackowski, S. / Park, H.W.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A.
Authors: Yun, M. / Park, C.G. / Kim, J.Y. / Rock, C.O. / Jackowski, S. / Park, H.W.
History
DepositionApr 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PANTOTHENATE KINASE
B: PANTOTHENATE KINASE
C: PANTOTHENATE KINASE
D: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0068
Polymers146,9364
Non-polymers3,0704
Water5,423301
1
A: PANTOTHENATE KINASE
B: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0034
Polymers73,4682
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-33 kcal/mol
Surface area26410 Å2
MethodPISA
2
C: PANTOTHENATE KINASE
D: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0034
Polymers73,4682
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-26 kcal/mol
Surface area26340 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-68 kcal/mol
Surface area50940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.00, 71.24, 87.68
Angle α, β, γ (deg.)102.44, 89.48, 93.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PANTOTHENATE KINASE / PANK


Mass: 36733.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6I3, pantothenate kinase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, isopropanol, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
21 mMdithiothreitol1drop
31 mMEDTA1drop
420 mg/mlprotein1drop
52 mMAMPPNP1drop
611 %PEG80001reservoir
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Nov 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 46593 / Num. obs: 46593 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.129 / Num. unique all: 1344 / % possible all: 52.7
Reflection
*PLUS
Num. measured all: 335425
Reflection shell
*PLUS
% possible obs: 52.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→50 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 2071 -RANDOM
Rwork0.2013 ---
all-41211 --
obs-41211 81.44 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9980 0 192 301 10473
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.594
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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