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- PDB-4d57: Understanding bi-specificity of A-domains -

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Basic information

Entry
Database: PDB / ID: 4d57
TitleUnderstanding bi-specificity of A-domains
ComponentsAPNA A1
KeywordsTRANSCRIPTION / NON-RIBOSOMAL PEPTIDE SYNTHETASE / ADENYLATION / A DOMAIN
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
AMP-binding / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 ...AMP-binding / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ARGININE / PHOSPHATE ION / ApnAA1
Similarity search - Component
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKaljunen, H. / Schiefelbein, S.H.H. / Stummer, D. / Kozak, S. / Meijers, R. / Christiansen, G. / Rentmeister, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structural Elucidation of the Bispecificity of a Domains as a Basis for Activating Non-Natural Amino Acids.
Authors: Kaljunen, H. / Schiefelbein, S.H.H. / Stummer, D. / Kozak, S. / Meijers, R. / Christiansen, G. / Rentmeister, A.
History
DepositionNov 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Data collection
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: APNA A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3926
Polymers64,5901
Non-polymers8025
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.142, 81.845, 89.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein APNA A1


Mass: 64590.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planktothrix agardhii (bacteria) / Strain: PCC7821 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0WVH3

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.9 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 6.5
Details: 24-30% POLYETHYLENE GLYCOL 3350 0.1 M MES OR BIS-TRIS PH 5.5 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2013
RadiationMonochromator: DOUBLE CRYSTAL(SI111, SI311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→89.7 Å / Num. obs: 34214 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 13 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.4 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMU

1amu


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22313 1714 5 %RANDOM
Rwork0.1784 ---
obs0.18062 32442 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.31 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 51 122 3981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194040
X-RAY DIFFRACTIONr_bond_other_d00.023904
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9825519
X-RAY DIFFRACTIONr_angle_other_deg3.66238984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11124.77174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48415694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.111521
X-RAY DIFFRACTIONr_chiral_restr0.1240.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214562
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02899
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_it2.9432.9131988
X-RAY DIFFRACTIONr_mcbond_other2.9362.9121987
X-RAY DIFFRACTIONr_mcangle_it3.934.3422499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5553.3612052
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: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 128 -
Rwork0.221 2345 -
obs--98.49 %

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