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- PDB-4d4h: Understanding bi-specificity of A-domains -

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Basic information

Entry
Database: PDB / ID: 4d4h
TitleUnderstanding bi-specificity of A-domains
ComponentsAPNAA1
KeywordsHYDROLASE / 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, 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...AMP-binding / 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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 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
DepositionOct 29, 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_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_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: APNAA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6822
Polymers64,5901
Non-polymers921
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.814, 81.190, 89.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein APNAA1 / 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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 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: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2013
RadiationMonochromator: DOUBLE CRYSTAL (SI111, SI311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→19.97 Å / Num. obs: 33645 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 35.78 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMU

1amu


Resolution: 2.019→19.97 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 1676 5.1 %
Rwork0.2041 --
obs0.2058 33052 98.42 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.019→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 6 108 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013314
X-RAY DIFFRACTIONf_angle_d1.3214525
X-RAY DIFFRACTIONf_dihedral_angle_d16.141237
X-RAY DIFFRACTIONf_chiral_restr0.091535
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0193-2.07870.42991210.33042233X-RAY DIFFRACTION85
2.0787-2.14570.26631220.23222618X-RAY DIFFRACTION100
2.1457-2.22230.26061230.21152635X-RAY DIFFRACTION100
2.2223-2.31110.26321580.20792590X-RAY DIFFRACTION99
2.3111-2.41610.24891450.20032610X-RAY DIFFRACTION100
2.4161-2.54330.23761310.19912645X-RAY DIFFRACTION100
2.5433-2.70230.26361460.19742616X-RAY DIFFRACTION100
2.7023-2.91030.22611340.21212639X-RAY DIFFRACTION99
2.9103-3.20210.26141470.21332650X-RAY DIFFRACTION100
3.2021-3.6630.25211500.2022648X-RAY DIFFRACTION99
3.663-4.60570.1871630.17282680X-RAY DIFFRACTION100
4.6057-19.97140.22581360.21372812X-RAY DIFFRACTION99

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