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- PDB-4w4t: The crystal structure of the terminal R domain from the myxalamid... -

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Basic information

Entry
Database: PDB / ID: 4w4t
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


catalytic activity / nucleotide binding
Similarity search - Function
TubC, N-terminal docking domain superfamily / TubC, N-terminal docking domain / 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 superfamily / TubC, N-terminal docking domain / 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, C-terminal domain superfamily / AMP-binding enzyme / 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
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 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
DepositionAug 15, 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)93,2474
Polymers93,1292
Non-polymers1182
Water16,826934
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-9 kcal/mol
Surface area33260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.838, 159.304, 54.897
Angle α, β, γ (deg.)90.00, 108.88, 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-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 934 / 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: 45.54 %
Description: Best quality diffracting crystals were SeMet. We used SeMet protein crystals for molecular replacement data collection.
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: SSRL / Beamline: BL12-2 / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 69238 / % possible obs: 98.1 % / Redundancy: 2.7 % / Net I/σ(I): 23
Reflection shellHighest resolution: 1.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.1 / Rsym value: 0.035 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD data set collected of the same MxaA Reductase construct

Resolution: 1.845→29.182 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2004 2.9 %
Rwork0.1747 --
obs0.1758 69221 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.845→29.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 8 934 6933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076119
X-RAY DIFFRACTIONf_angle_d1.0288306
X-RAY DIFFRACTIONf_dihedral_angle_d12.5372286
X-RAY DIFFRACTIONf_chiral_restr0.04958
X-RAY DIFFRACTIONf_plane_restr0.0051074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8449-1.8910.26921320.2214649X-RAY DIFFRACTION94
1.891-1.94210.27751470.21114720X-RAY DIFFRACTION97
1.9421-1.99930.28561430.20424730X-RAY DIFFRACTION97
1.9993-2.06380.26081440.19574824X-RAY DIFFRACTION99
2.0638-2.13750.22681440.19854848X-RAY DIFFRACTION99
2.1375-2.22310.23961430.19214832X-RAY DIFFRACTION98
2.2231-2.32420.22011360.18464779X-RAY DIFFRACTION98
2.3242-2.44670.23271500.18224763X-RAY DIFFRACTION97
2.4467-2.59990.2291330.18914849X-RAY DIFFRACTION99
2.5999-2.80050.24311470.18714854X-RAY DIFFRACTION99
2.8005-3.0820.22111480.18144785X-RAY DIFFRACTION98
3.082-3.52740.19551460.16824870X-RAY DIFFRACTION100
3.5274-4.44160.17631410.14854842X-RAY DIFFRACTION98
4.4416-29.18570.16631500.14974872X-RAY DIFFRACTION98

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