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- PDB-7a8y: X-ray crystal structure of Aspartate alpha-decarboxylase in compl... -

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Basic information

Entry
Database: PDB / ID: 7a8y
TitleX-ray crystal structure of Aspartate alpha-decarboxylase in complex with D-Serine
Components(Aspartate 1-decarboxylase) x 2
KeywordsLYASE / Decarboxylase
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / cytoplasm
Similarity search - Function
Aspartate decarboxylase / Aspartate decarboxylase / Aspartate decarboxylase-like domain superfamily
Similarity search - Domain/homology
D-SERINE / SERINE / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYorke, B.A. / Raskar, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110296/B/15/Z United Kingdom
CitationJournal: Phys Chem Chem Phys / Year: 2022
Title: Structure and diffusive dynamics of aspartate alpha-decarboxylase (ADC) liganded with D-serine in aqueous solution.
Authors: Raskar, T. / Niebling, S. / Devos, J.M. / Yorke, B.A. / Hartlein, M. / Huse, N. / Forsyth, V.T. / Seydel, T. / Pearson, A.R.
History
DepositionAug 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Data collection / Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / diffrn_source
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Sep 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly_seq / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 3.1Nov 6, 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
AAA: Aspartate 1-decarboxylase
BBB: Aspartate 1-decarboxylase
DDD: Aspartate 1-decarboxylase
EaE: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0349
Polymers26,5524
Non-polymers4825
Water3,747208
1
AAA: Aspartate 1-decarboxylase
BBB: Aspartate 1-decarboxylase
DDD: Aspartate 1-decarboxylase
EaE: Aspartate 1-decarboxylase
hetero molecules

AAA: Aspartate 1-decarboxylase
BBB: Aspartate 1-decarboxylase
DDD: Aspartate 1-decarboxylase
EaE: Aspartate 1-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,06918
Polymers53,1048
Non-polymers96510
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area23650 Å2
ΔGint-114 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.300, 71.300, 216.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein/peptide / Protein , 2 types, 4 molecules AAADDDBBBEaE

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


Mass: 3056.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Modification at residue 25: Serine and pyrovoyl residues are present with partial occupancies.
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: panD, BON96_17415, D9J78_12565, FKO60_12525, G5697_15675
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y8GT61, aspartate 1-decarboxylase
#2: Protein Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase


Mass: 10219.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Some of the terminal residues are not modeled due to missing density
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: panD, BON96_17415, D9J78_12565, FKO60_12525, G5697_15675
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y8GT61, aspartate 1-decarboxylase

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Non-polymers , 4 types, 213 molecules

#3: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 1.8 M ammonium sulphate, 100 mM sodium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.75→46.98 Å / Num. obs: 33922 / % possible obs: 99.99 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.02384 / Net I/σ(I): 21.5
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.1564 / Mean I/σ(I) obs: 5.25 / Num. unique obs: 3301 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AW8

1aw8


Resolution: 1.75→46.975 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.165 / SU B: 1.67 / SU ML: 0.054 / Average fsc free: 0.9557 / Average fsc work: 0.9597 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1905 1702 5.017 %
Rwork0.1705 32220 -
all0.171 --
obs-33922 99.988 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.673 Å2
Baniso -1Baniso -2Baniso -3
1-0.257 Å20.129 Å20 Å2
2--0.257 Å2-0 Å2
3----0.835 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 40 208 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131997
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171838
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.6392712
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5874243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.8255.227264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11321.887106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10615320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6981515
X-RAY DIFFRACTIONr_chiral_restr0.0530.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined0.2080.2352
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21676
X-RAY DIFFRACTIONr_nbtor_refined0.1480.2927
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2150
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1580.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.227
X-RAY DIFFRACTIONr_nbd_other0.2460.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.221
X-RAY DIFFRACTIONr_mcbond_it1.1112.0821011
X-RAY DIFFRACTIONr_mcbond_other1.1112.0821011
X-RAY DIFFRACTIONr_mcangle_it1.9393.0831264
X-RAY DIFFRACTIONr_mcangle_other1.9393.0841265
X-RAY DIFFRACTIONr_scbond_it1.3172.244985
X-RAY DIFFRACTIONr_scbond_other1.3172.245986
X-RAY DIFFRACTIONr_scangle_it2.1583.3011441
X-RAY DIFFRACTIONr_scangle_other2.1573.3021442
X-RAY DIFFRACTIONr_lrange_it5.32225.3142185
X-RAY DIFFRACTIONr_lrange_other5.32125.3212186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2361120.2122352X-RAY DIFFRACTION100
1.795-1.8450.21270.1992237X-RAY DIFFRACTION99.9577
1.845-1.8980.211100.1922199X-RAY DIFFRACTION100
1.898-1.9560.1921060.1862153X-RAY DIFFRACTION100
1.956-2.020.1861170.1672089X-RAY DIFFRACTION100
2.02-2.0910.181950.1672037X-RAY DIFFRACTION100
2.091-2.170.189950.1671955X-RAY DIFFRACTION100
2.17-2.2590.1821040.161880X-RAY DIFFRACTION100
2.259-2.3590.1441120.1591798X-RAY DIFFRACTION100
2.359-2.4740.2041030.1631735X-RAY DIFFRACTION100
2.474-2.6070.181710.1671663X-RAY DIFFRACTION100
2.607-2.7650.143780.1581593X-RAY DIFFRACTION100
2.765-2.9560.19760.1591494X-RAY DIFFRACTION100
2.956-3.1920.203800.1661381X-RAY DIFFRACTION100
3.192-3.4960.155650.1621305X-RAY DIFFRACTION100
3.496-3.9070.205630.1521185X-RAY DIFFRACTION100
3.907-4.5080.147620.1371056X-RAY DIFFRACTION100
4.508-5.5140.237580.171910X-RAY DIFFRACTION100
5.514-7.7670.275430.231737X-RAY DIFFRACTION100
7.767-9.50.288250.234462X-RAY DIFFRACTION99.3878

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