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Basic information

Entry
Database: PDB / ID: 4crz
TitleDirect visualisation of strain-induced protein prost-translational modification
Components
  • ASPARTATE 1-DECARBOXYLASE
  • PANZ
KeywordsLYASE / COENZYME A / RADIATION DAMAGE / PANTOTHENATE
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 / Gcn5-related N-acetyltransferase (GNAT) / Aspartate decarboxylase-like domain superfamily / 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 / Gcn5-related N-acetyltransferase (GNAT) / Aspartate decarboxylase-like domain superfamily / 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
ACETYL COENZYME *A / THIOCYANATE ION / Aspartate 1-decarboxylase / PanD regulatory factor
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMonteiro, D.C.F. / Patel, V. / Bartlett, C.P. / Grant, T.D. / Nozaki, S. / Gowdy, J.A. / Snell, E.H. / Niki, H. / Pearson, A.R. / Webb, M.E.
CitationJournal: Chem.Biol. / Year: 2015
Title: The Structure of the Pand/Panz Protein Complex Reveals Negative Feedback Regulation of Pantothenate Biosynthesis by Coenzyme A.
Authors: Monteiro, D.C. / Patel, V. / Bartlett, C.P. / Nozaki, S. / Grant, T.D. / Gowdy, J.A. / Thompson, G.S. / Kalverda, A.P. / Snell, E.H. / Niki, H. / Pearson, A.R. / Webb, M.E.
History
DepositionMar 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE 1-DECARBOXYLASE
B: PANZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4255
Polymers31,5332
Non-polymers8923
Water2,612145
1
A: ASPARTATE 1-DECARBOXYLASE
B: PANZ
hetero molecules

A: ASPARTATE 1-DECARBOXYLASE
B: PANZ
hetero molecules

A: ASPARTATE 1-DECARBOXYLASE
B: PANZ
hetero molecules

A: ASPARTATE 1-DECARBOXYLASE
B: PANZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,69920
Polymers126,1318
Non-polymers3,56812
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area19970 Å2
ΔGint-72.4 kcal/mol
Surface area49990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.280, 86.280, 80.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ASPARTATE 1-DECARBOXYLASE / ASPARTATE ALPHA-DECARBOXYLASE


Mass: 15793.928 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PRSETA-ADC(T57V) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): MG1655 PAND-PANZ-(DE3) / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Protein PANZ


Mass: 15738.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PET28A-PANZ / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): MG1655 PAND-PANZ-(DE3) / References: UniProt: P37613

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Non-polymers , 4 types, 148 molecules

#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsHEXAHIS-TAGGED ADC. POINT MUTATION T57V. C-TERMINAL HEXAHIS-TAGGED PANZ.

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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.4
Details: 20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2013 / Details: VARIMAX OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.7→33.7 Å / Num. obs: 32244 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AZD

4azd


Resolution: 1.7→29.52 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.563 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY RELEVANT HETEROOCTAMER IS FORMED BY APPLICATION OF THE CRYSTALLOGRAPHIC 4-FOLD SYMMETRY AXIS TO THE ASYMMETRIC UNIT CELL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY RELEVANT HETEROOCTAMER IS FORMED BY APPLICATION OF THE CRYSTALLOGRAPHIC 4-FOLD SYMMETRY AXIS TO THE ASYMMETRIC UNIT CELL CONTENTS. EACH ASU CONTAINS ONE ADC PROTOMER AND ONE PANZ PROTOMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.17519 1633 5.1 %RANDOM
Rwork0.14458 ---
obs0.14611 30609 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 55 145 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192175
X-RAY DIFFRACTIONr_bond_other_d0.0020.022084
X-RAY DIFFRACTIONr_angle_refined_deg2.3331.972958
X-RAY DIFFRACTIONr_angle_other_deg0.9773.0014771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6823.113106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01515378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3081524
X-RAY DIFFRACTIONr_chiral_restr0.1440.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
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_it2.6552.0161043
X-RAY DIFFRACTIONr_mcbond_other2.6522.011039
X-RAY DIFFRACTIONr_mcangle_it3.9313.0131302
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1722.4781132
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 122 -
Rwork0.327 2242 -
obs--99.66 %

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