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- PDB-6qkb: Crystal structure of the beta-hydroxyaspartate aldolase of Paraco... -

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Basic information

Entry
Database: PDB / ID: 6qkb
TitleCrystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans
ComponentsD-3-hydroxyaspartate aldolase
KeywordsLYASE / beta-hydroxyaspartate aldolase
Function / homology
Function and homology information


3-hydroxy-D-aspartate aldolase / glycolate catabolic process / oxo-acid-lyase activity / glyoxylate catabolic process / pyridoxal phosphate binding / magnesium ion binding
Similarity search - Function
D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel ...D-serine dehydratase-like domain / D-serine dehydratase-like domain / D-serine dehydratase-like domain superfamily / Putative serine dehydratase domain / Putative serine dehydratase domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 3-hydroxy-D-aspartate aldolase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 Å
AuthorsZarzycki, J. / Schada von Borzyskowski, L. / Gilardet, A. / Erb, T.J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB987 Germany
European UnionFET686330 Germany
CitationJournal: Nature / Year: 2019
Title: Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.
Authors: Schada von Borzyskowski, L. / Severi, F. / Kruger, K. / Hermann, L. / Gilardet, A. / Sippel, F. / Pommerenke, B. / Claus, P. / Cortina, N.S. / Glatter, T. / Zauner, S. / Zarzycki, J. / ...Authors: Schada von Borzyskowski, L. / Severi, F. / Kruger, K. / Hermann, L. / Gilardet, A. / Sippel, F. / Pommerenke, B. / Claus, P. / Cortina, N.S. / Glatter, T. / Zauner, S. / Zarzycki, J. / Fuchs, B.M. / Bremer, E. / Maier, U.G. / Amann, R.I. / Erb, T.J.
History
DepositionJan 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-3-hydroxyaspartate aldolase
B: D-3-hydroxyaspartate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2256
Polymers83,6822
Non-polymers5434
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-25 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.598, 75.247, 157.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-3-hydroxyaspartate aldolase / beta-hydroxyaspartate aldolase


Mass: 41841.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: Pden_3919 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): AI
References: UniProt: A1B8Z1, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.7 % / Description: thick plate
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: The protein (10 mg/mL) in buffer (25 mM Tris/HCl pH 8.0, 100 mM NaCl, 1 mM MgCl2, 0.01 mM PLP, 0.1 mM DTT) was mixed in a 1:1 ratio with crystallization condition (0.2 M ammonium chloride pH ...Details: The protein (10 mg/mL) in buffer (25 mM Tris/HCl pH 8.0, 100 mM NaCl, 1 mM MgCl2, 0.01 mM PLP, 0.1 mM DTT) was mixed in a 1:1 ratio with crystallization condition (0.2 M ammonium chloride pH 6.3, 20% w/v polyethylene glycol 3,350).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.701→29.027 Å / Num. obs: 87281 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Rsym value: 0.134 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.701-1.796.50.8581.9124770.7080.3580.93199
5.38-29.0276.10.04527.730010.9990.020.0599.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V15

4v15


Resolution: 1.701→29.027 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 16.81
RfactorNum. reflection% reflection
Rfree0.1765 1998 2.29 %
Rwork0.1576 --
obs0.158 87194 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.41 Å2 / Biso mean: 18.8706 Å2 / Biso min: 7.69 Å2
Refinement stepCycle: final / Resolution: 1.701→29.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 32 822 6663
Biso mean--23.76 31.58 -
Num. residues----767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7013-1.74380.24831390.23365909604898
1.7438-1.7910.26291410.21375995613699
1.791-1.84360.231400.198960086148100
1.8436-1.90310.20421420.188660186160100
1.9031-1.97110.20691420.173360386180100
1.9711-2.05010.17941410.161860456186100
2.0501-2.14330.17561410.153160456186100
2.1433-2.25630.19671420.154760436185100
2.2563-2.39760.15521420.157360996241100
2.3976-2.58260.21771440.150661086252100
2.5826-2.84230.16821430.155460956238100
2.8423-3.25310.15541440.149261546298100
3.2531-4.09670.15061460.13761976343100
4.0967-29.03110.15361510.147364426593100
Refinement TLS params.Method: refined / Origin x: 17.0683 Å / Origin y: 49.7931 Å / Origin z: 57.7976 Å
111213212223313233
T0.0982 Å20.002 Å2-0.0004 Å2-0.1079 Å2-0.0029 Å2--0.0852 Å2
L0.2194 °2-0.0598 °20.0052 °2-0.3203 °2-0.0121 °2--0.1277 °2
S0.0022 Å °0 Å °-0.006 Å °0.0306 Å °0.0043 Å °-0.0024 Å °0.0063 Å °0.0035 Å °-0.0068 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 387
2X-RAY DIFFRACTION1ALLA401 - 879
3X-RAY DIFFRACTION1ALLB5 - 387
4X-RAY DIFFRACTION1ALLB401 - 943

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