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

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Basic information

Entry
Database: PDB / ID: 1esn
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Pantothenate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 1.0Nov 17, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _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

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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)149,05812
Polymers146,9364
Non-polymers2,1228
Water5,513306
1
A: PANTOTHENATE KINASE
B: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5296
Polymers73,4682
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-51 kcal/mol
Surface area27150 Å2
MethodPISA
2
C: PANTOTHENATE KINASE
D: PANTOTHENATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5296
Polymers73,4682
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-50 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.08, 130.08, 281.75
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 4.68 Å3/Da / Density % sol: 73.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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: 0.9791
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Nov 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 84985 / Num. obs: 84985 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.4 / Num. unique all: 4029 / % possible all: 95.8
Reflection
*PLUS
Num. measured all: 1100377
Reflection shell
*PLUS
% possible obs: 95.8 % / Mean I/σ(I) obs: 15.1

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Processing

Software
NameClassification
SOLVEphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→50 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 --RANDOM
Rwork0.216 ---
all-72353 --
obs-72353 84.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10064 0 128 306 10498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.66
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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