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- PDB-6rxh: In-flow serial synchrotron crystallography using a 3D-printed mic... -

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Basic information

Entry
Database: PDB / ID: 6rxh
TitleIn-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-MiXD): Aspartate alpha-decarboxylase
Components(Aspartate 1-decarboxylase) x 2
KeywordsLYASE
Function / homology
Function and homology information


alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / pantothenate biosynthetic process / protein autoprocessing / cytoplasm / 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
Aspartate 1-decarboxylase / Aspartate 1-decarboxylase / Aspartate 1-decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMonteiro, D.C.F. / von Stetten, D. / Pearson, A.R. / Trebbin, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEXC 1074 - projectID 194651731 Germany
German Federal Ministry for Education and Research05K16GUI Germany
CitationJournal: Iucrj / Year: 2020
Title: 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow.
Authors: Monteiro, D.C.F. / von Stetten, D. / Stohrer, C. / Sans, M. / Pearson, A.R. / Santoni, G. / van der Linden, P. / Trebbin, M.
History
DepositionJun 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
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 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Dec 13, 2023Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.3Nov 20, 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: Aspartate 1-decarboxylase
D: Aspartate 1-decarboxylase
E: Aspartate 1-decarboxylase


Theoretical massNumber of molelcules
Total (without water)31,56211
Polymers31,5624
Non-polymers07
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-57 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 72.800, 219.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 4770.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ADC beta-chain after post-translational modification
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panD, DNX30_02475 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A403CTL2, UniProt: P0A790*PLUS, aspartate 1-decarboxylase
#2: Protein Aspartate 1-decarboxylase / Aspartate alpha-decarboxylase


Mass: 11010.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ADC alpha-chain after post-translational modification
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: panD, DN623_10270 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A3U0WEI2, UniProt: P0A790*PLUS, aspartate 1-decarboxylase
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52.78 % / Description: cuboid microcrystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 3.8
Details: 1:3 protein:mother liquor mixture. 25 mg/mL of ADC in 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.1 mM DTT. Mother liquor: 1.95 M (NH4)2SO4, 100 mM citrate/di-sodium phosphate buffer pH 3.8

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2→63.05 Å / Num. obs: 24287 / % possible obs: 100 % / Redundancy: 6006 % / Biso Wilson estimate: 30.5 Å2 / R split: 0.04 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.08 Å / Redundancy: 4356 % / Num. unique obs: 2374 / R split: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
MOLREP11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AW8

1aw8


Resolution: 2→63.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.699 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18432 1277 5.3 %RANDOM
Rwork0.15183 ---
obs0.15357 22918 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.161 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→63.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 7 96 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131940
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171786
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.6372626
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5814118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.8345.294255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.59521.284109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91215316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0931516
X-RAY DIFFRACTIONr_chiral_restr0.080.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02425
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_it3.6373.534976
X-RAY DIFFRACTIONr_mcbond_other3.6333.53975
X-RAY DIFFRACTIONr_mcangle_it4.9355.2431216
X-RAY DIFFRACTIONr_mcangle_other4.9375.2461217
X-RAY DIFFRACTIONr_scbond_it4.9864.146963
X-RAY DIFFRACTIONr_scbond_other4.9844.151964
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5915.9961406
X-RAY DIFFRACTIONr_long_range_B_refined9.46539.7091931
X-RAY DIFFRACTIONr_long_range_B_other9.43139.6661923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 89 -
Rwork0.252 1655 -
obs--99.94 %

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