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- PDB-5g4j: Phospholyase A1RDF1 from Arthrobacter in complex with phosphoetha... -

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Basic information

Entry
Database: PDB / ID: 5g4j
TitlePhospholyase A1RDF1 from Arthrobacter in complex with phosphoethanolamine
ComponentsPUTATIVE AMINOTRANSFERASE CLASS III PROTEIN
KeywordsLYASE / PYRIDOXAL PHOSPHATE / TRANSAMINASE / PHOSPHOLYASE
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EXT / Putative Aminotransferase class III protein
Similarity search - Component
Biological speciesARTHROBACTER AURESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsCuetos, A. / Tuan, A.N. / Mangas Sanchez, J. / Grogan, G.
CitationJournal: Chembiochem / Year: 2016
Title: Structural Basis for Phospholyase Activity of a Class III Transaminase Homologue.
Authors: Cuetos, A. / Steffen-Munsberg, F. / Mangas Sanchez, J. / Frese, A. / Bornscheuer, U.T. / Hohne, M. / Grogan, G.
History
DepositionMay 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE AMINOTRANSFERASE CLASS III PROTEIN
B: PUTATIVE AMINOTRANSFERASE CLASS III PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9927
Polymers96,1832
Non-polymers8095
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-90.7 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.166, 96.371, 121.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (0.2304, -0.4739, 0.8499), (-0.4704, -0.8188, -0.329), (0.8519, -0.324, -0.4116)
Vector: 26.18, -11.26, -44.2)

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Components

#1: Protein PUTATIVE AMINOTRANSFERASE CLASS III PROTEIN


Mass: 48091.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTHROBACTER AURESCENS (bacteria) / Strain: TC1 / Plasmid: PET-YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A1RDF1, ethanolamine-phosphate phospho-lyase
#2: Chemical ChemComp-EXT / {5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate


Mass: 370.190 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O9P2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6
Details: 24% (W/V) PEG 3350, 0.2 M (NH4)2SO4 AND 3% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.1 M BIS-TRIS PROPANE BUFFER AT PH 6.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.87→64.59 Å / Num. obs: 74689 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 1.87→1.95 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G4I

5g4i


Resolution: 1.87→75.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.77 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19943 3636 4.9 %RANDOM
Rwork0.16731 ---
obs0.16884 70978 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.913 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0 Å2-0 Å2
2--0.51 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.87→75.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 49 476 6825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0196494
X-RAY DIFFRACTIONr_bond_other_d0.0080.026175
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9758831
X-RAY DIFFRACTIONr_angle_other_deg1.4783.00114127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88523.282259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11815998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5961547
X-RAY DIFFRACTIONr_chiral_restr0.2270.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217445
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021477
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_it2.3822.4683382
X-RAY DIFFRACTIONr_mcbond_other2.3812.4663381
X-RAY DIFFRACTIONr_mcangle_it3.0813.6844225
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1272.7353112
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: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 240 -
Rwork0.242 5226 -
obs--99.84 %

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