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- PDB-1gn8: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Mn2+ATP FR... -

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Basic information

Entry
Database: PDB / ID: 1gn8
TitlePHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Mn2+ATP FROM ESCHERICHIA COLI
ComponentsPHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / COENZYME A BIOSYNTHESIS / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsIzard, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The Crystal Structures of Phosphopantetheine Adenylyltransferase with Bound Substrates Reveal the Enzyme'S Catalytic Mechanism
Authors: Izard, T.
History
DepositionOct 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1329
Polymers35,7192
Non-polymers1,4127
Water4,450247
1
A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules

A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules

A: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
B: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,39527
Polymers107,1586
Non-polymers4,23721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
Unit cell
Length a, b, c (Å)135.060, 135.060, 135.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE


Mass: 17859.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli)
References: UniProt: P23875, UniProt: P0A6I6*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.88 Å3/Da / Density % sol: 60 %
Crystal growpH: 5 / Details: pH 5.00
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Izard, T., (1999) Acta Crystallog., D55, 1226. / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH8.
20.5 mMdithiothreitol1drop
318 mg/mlprotein1drop
41.1 Mammonium sulfate1reservoir
50.2 M1reservoirNaCl
6100 mMsodium acetate1reservoirpH5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP / Detector: IMAGE PLATE / Date: Jul 21, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→20 Å / Num. obs: 35949 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 12.351 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 17.8
Reflection shellResolution: 1.82→1.82 Å / Rmerge(I) obs: 0.495 / % possible all: 77.8
Reflection
*PLUS
% possible obs: 96.9 % / Num. measured all: 444009 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
% possible obs: 77.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1B6T

1b6t


Resolution: 1.83→21.91 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1774 5 %RANDOM
Rwork0.229 ---
obs0.229 35800 99 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.83→21.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 79 247 2832
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 282 5.3 %
Rwork0.338 5625 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION3DPC.PARDPC.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 35859
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor obs: 0.338

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