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- PDB-4u7w: The crystal structure of the terminal R domain from the myxalamid... -

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Basic information

Entry
Database: PDB / ID: 4u7w
TitleThe crystal structure of the terminal R domain from the myxalamid PKS-NRPS biosynthetic pathway
ComponentsMxaA
KeywordsOXIDOREDUCTASE / Reductase / thioesterase / Rossmann fold / polyketide / non-ribosomal peptide / polyketide synthase / non-ribosomal peptide synthetase / short-chain dehydrogenases
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / catalytic activity / nucleotide binding / cytosol
Similarity search - Function
TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain ...TubC, N-terminal docking domain / TubC, N-terminal docking domain superfamily / TubC N-terminal docking domain / Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-NDP / MxaA
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsTsai, S.C. / Keasling, J.D. / Luo, R. / Barajas, J.F. / Phelan, R.M. / Schaub, A.J. / Kliewer, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM100305-03 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5F31GM100738-02 United States
CitationJournal: Chem.Biol. / Year: 2015
Title: Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols.
Authors: Barajas, J.F. / Phelan, R.M. / Schaub, A.J. / Kliewer, J.T. / Kelly, P.J. / Jackson, D.R. / Luo, R. / Keasling, J.D. / Tsai, S.C.
History
DepositionJul 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MxaA
B: MxaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7386
Polymers93,1292
Non-polymers1,6094
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-15 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.106, 159.050, 51.184
Angle α, β, γ (deg.)90.00, 106.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MxaA


Mass: 46564.414 Da / Num. of mol.: 2 / Fragment: UNP residues 1115-1513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: mxaA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93TX2
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.22M Ammonium Acetate, 28% PEG 3350, 0.1M Hepes pH.7.7
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9775 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 61578 / % possible obs: 100 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.211 / Rsym value: 0.083 / Net I/σ(I): 9.3
Reflection shellHighest resolution: 1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.93 / Rsym value: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD data set of the same MxaA Reductase construct

Resolution: 1.899→41.82 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.83 / Stereochemistry target values: TWIN_LSQ_F
Details: Good quality data could only be collected with SeMet crystals. We initially solved the structure by MAD and used SeMet crystals to collect single wavelength experiments for molecular replacement.
RfactorNum. reflection% reflection
Rfree0.2034 1997 3.25 %
Rwork0.1582 --
obs0.1617 61518 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 104 502 6640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086275
X-RAY DIFFRACTIONf_angle_d0.9768540
X-RAY DIFFRACTIONf_dihedral_angle_d14.7972366
X-RAY DIFFRACTIONf_chiral_restr0.036980
X-RAY DIFFRACTIONf_plane_restr0.0041097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9004-1.94790.29281410.26594172X-RAY DIFFRACTION97
1.9479-2.00050.28981460.24934218X-RAY DIFFRACTION97
2.0005-2.05940.25631430.24194287X-RAY DIFFRACTION97
2.0594-2.12580.25261420.23854256X-RAY DIFFRACTION97
2.1258-2.20180.241400.23464216X-RAY DIFFRACTION97
2.2018-2.28990.22671420.21454231X-RAY DIFFRACTION97
2.2899-2.3940.30091410.21054245X-RAY DIFFRACTION97
2.394-2.52020.27231470.19734251X-RAY DIFFRACTION97
2.5202-2.67790.20021440.1874268X-RAY DIFFRACTION97
2.6779-2.88450.20551420.18054232X-RAY DIFFRACTION97
2.8845-3.17430.19881400.15914258X-RAY DIFFRACTION97
3.1743-3.63270.18181410.12924281X-RAY DIFFRACTION97
3.6327-4.5730.15151430.10094245X-RAY DIFFRACTION97
4.573-26.59040.17261430.10164300X-RAY DIFFRACTION97

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