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- PDB-5ls7: Complex of wild type E. coli alpha aspartate decarboxylase with i... -

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Basic information

Entry
Database: PDB / ID: 5ls7
TitleComplex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ
Components
  • (Aspartate 1-decarboxylase) x 2
  • PanD maturation factor
KeywordsLYASE / protein derived cofactor / coenzyme A biosynthesis / protein complex / metabolic pathway regulation
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / acetyl-CoA binding / pantothenate biosynthetic process / zymogen activation / acyltransferase activity, transferring groups other than amino-acyl groups / protein autoprocessing / protein processing / cytosol
Similarity search - Function
PanD regulatory factor PanZ / PanZ, acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain, PanZ / Aspartate decarboxylase / Aspartate decarboxylase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...PanD regulatory factor PanZ / PanZ, acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain, PanZ / Aspartate decarboxylase / Aspartate decarboxylase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
methyl radical / ACETYL COENZYME *A / CARBON DIOXIDE / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Aspartate 1-decarboxylase / PanD regulatory factor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsMonteiro, D.C.F. / Webb, M.E. / Pearson, A.R.
Funding support United Kingdom, Germany, 4items
OrganizationGrant numberCountry
Wellcome Trust096684/Z/11/Z United Kingdom
Wellcome Trust105615/Z/14/Z United Kingdom
German Research FoundationExcellence Cluster: Hamburg Centre for Ultrafast Imaging Germany
Wellcome Trust094232/Z/10/Z United Kingdom
CitationJournal: Biochemistry / Year: 2017
Title: The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZAcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan).
Authors: Arnott, Z.L.P. / Nozaki, S. / Monteiro, D.C.F. / Morgan, H.E. / Pearson, A.R. / Niki, H. / Webb, M.E.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate 1-decarboxylase
B: PanD maturation factor
D: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04715
Polymers31,5543
Non-polymers1,49412
Water5,260292
1
A: Aspartate 1-decarboxylase
B: PanD maturation factor
D: Aspartate 1-decarboxylase
hetero molecules

A: Aspartate 1-decarboxylase
B: PanD maturation factor
D: Aspartate 1-decarboxylase
hetero molecules

A: Aspartate 1-decarboxylase
B: PanD maturation factor
D: Aspartate 1-decarboxylase
hetero molecules

A: Aspartate 1-decarboxylase
B: PanD maturation factor
D: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,18960
Polymers126,21512
Non-polymers5,97448
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)85.863, 85.863, 80.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Aspartate 1-decarboxylase / / Aspartate alpha-decarboxylase


Mass: 4770.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-17 are the purification tag. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: panD, b0131, JW0127 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A790, aspartate 1-decarboxylase

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Protein , 2 types, 2 molecules BD

#2: Protein PanD maturation factor


Mass: 15738.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminus is not visible in the electron density
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: panM, panZ, yhhK, b3459, JW3424 / Production host: Escherichia coli (E. coli) / References: UniProt: P37613
#3: Protein Aspartate 1-decarboxylase / / Aspartate alpha-decarboxylase


Mass: 11044.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal residue is a pyruvoyl moiety formed after post-translation backbone cleavage after protein folding. Cysteine 78 is oxidised.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: panD, b0131, JW0127 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A790, aspartate 1-decarboxylase

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Non-polymers , 8 types, 304 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO2
#9: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#10: Chemical ChemComp-74C / methyl radical / Methane


Mass: 15.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCO2 derives from the sidechains of GLU B 70 and D 113 which have decomposed due to radiation damage. ...CO2 derives from the sidechains of GLU B 70 and D 113 which have decomposed due to radiation damage. 74C methyl radical derives from MET D114 as a result of radiation damage

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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: 2.46 Å3/Da / Density % sol: 50.01 % / Description: Bipyrimidal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM KSCN, 100 mM Bis-Tris propane pH 6.5, 20% v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.16→29.28 Å / Num. obs: 99822 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.1 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CRY

4cry


Resolution: 1.16→29.28 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.992 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13688 4966 5 %RANDOM
Rwork0.11341 ---
obs0.11458 94485 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.16→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 89 292 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0192259
X-RAY DIFFRACTIONr_bond_other_d0.0020.022172
X-RAY DIFFRACTIONr_angle_refined_deg2.8511.9823071
X-RAY DIFFRACTIONr_angle_other_deg1.2134983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7722.617107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03815394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1791527
X-RAY DIFFRACTIONr_chiral_restr0.1640.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022554
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3632.4281064
X-RAY DIFFRACTIONr_mcbond_other2.3521059
X-RAY DIFFRACTIONr_mcangle_it3.1091334
X-RAY DIFFRACTIONr_mcangle_other3.111335
X-RAY DIFFRACTIONr_scbond_it3.7291195
X-RAY DIFFRACTIONr_scbond_other3.6921190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8781717
X-RAY DIFFRACTIONr_long_range_B_refined5.472538
X-RAY DIFFRACTIONr_long_range_B_other5.4692539
X-RAY DIFFRACTIONr_rigid_bond_restr9.89332015
X-RAY DIFFRACTIONr_sphericity_free29.0735182
X-RAY DIFFRACTIONr_sphericity_bonded15.71252055
LS refinement shellResolution: 1.161→1.191 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 391 -
Rwork0.196 6688 -
obs--95.78 %

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