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- PDB-4d7z: E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resoluti... -

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Basic information

Entry
Database: PDB / ID: 4d7z
TitleE. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms
Components
  • ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
  • ASPARTATE 1-DECARBOXYLASE BETA CHAIN
KeywordsLYASE / PROTEIN DERIVED COFACTOR / PANTOTHENATE SYNTHESIS / PYRUVOYL COFACTOR / BETA-ALANINE
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / cytosol
Similarity search - Function
Aspartate decarboxylase / Aspartate decarboxylase / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBravo, J.P.K. / Monteiro, D.C.F. / Webb, M.E. / Pearson, A.R.
CitationJournal: To be Published
Title: The Structure of the E. Coli L-Aspartate-Alpha-Decarboxylase Mutant N72Q to a Resolution of 1.9 Angstroms
Authors: Bravo, J.P.K. / Monteiro, D.C.F. / Webb, M.E. / Pearson, A.R.
History
DepositionDec 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 13, 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 BETA CHAIN
B: ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3385
Polymers15,1162
Non-polymers2223
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-16.1 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.350, 71.350, 112.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2008-

HOH

21B-2010-

HOH

31B-2052-

HOH

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Components

#1: Protein/peptide ASPARTATE 1-DECARBOXYLASE BETA CHAIN


Mass: 4770.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PRCETA-ADC(N72Q) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DELTA PAND, DELTA PANZ, DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#2: Protein ASPARTATE 1-DECARBOXYLASE ALPHA CHAIN


Mass: 10345.524 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-119 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUE 25 IS A COVALENTLY LINKED PYRUVOYL COFACTOR, DERIVED FROM POSTTRANSLATIONAL MODIFICATION OF THE ZYMOGEN.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PRCETA-ADC(N72Q) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DELTA PAND, DELTA PANZ, DE3 / References: UniProt: P0A790, aspartate 1-decarboxylase
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAIN A CORRESPONDS TO RESIDUES 1-24 OF THE PAND (ZYMOGEN) SEQUENCE. FORMED AFTER BACKBONE CLEAVAGE ...CHAIN A CORRESPONDS TO RESIDUES 1-24 OF THE PAND (ZYMOGEN) SEQUENCE. FORMED AFTER BACKBONE CLEAVAGE AS PART OF ENZYME MATURATION. THIS SEQUENCE INCLUDES THE N-TERMINAL PURIFICATION TAG (17 RESIDUES) CHAIN B CORRESPONDS TO RESIDUES 25-119 OF THE PAND ( ZYMOGEN) SEQUENCE. FORMED AFTER BACKBONE CLEAVAGE AS PART OF ENZYME MATURATION. RESIDUE 25 IS A POSTTRANSLATIONALLY FORMED PYRUVOYL COFACTOR. ALSO CONTAINS MUTATION N72Q.

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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: 2.38 Å3/Da / Density % sol: 48.4 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 ...Details: ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 MM DTT. THIS WAS MIXED IN A 1:1 RATIO WITH RESERVOIR SOLUTION (0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS- TRIS PROPANE PH 6.8, 20 % W/V PEG 3350) AND CRYSTALLIZED BY HANGING DROP VAOUR DIFFUSION (4 UL DROPLET OVER A 1 ML RESERVOIR).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 2, 2014 / Details: VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→23.26 Å / Num. obs: 11805 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AW8

1aw8


Resolution: 1.9→60.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.122 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY SIDE CHAIN OF RESIDUE Y22 IS NOT MODELLED BEYOND C-BETA DUE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY SIDE CHAIN OF RESIDUE Y22 IS NOT MODELLED BEYOND C-BETA DUE TO LACK OF CLEAR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24418 552 4.7 %RANDOM
Rwork0.18622 ---
obs0.18894 11235 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 13 122 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019981
X-RAY DIFFRACTIONr_bond_other_d0.0010.02960
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9351319
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0022169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23223.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5115163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.197159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
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_it2.0392.194495
X-RAY DIFFRACTIONr_mcbond_other2.0292.181492
X-RAY DIFFRACTIONr_mcangle_it2.9683.25615
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2442.574486
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 50 -
Rwork0.285 798 -
obs--100 %

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