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- PDB-4z38: Crystal structure of enoyl reductase domain of MlnA from the macr... -

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Basic information

Entry
Database: PDB / ID: 4z38
TitleCrystal structure of enoyl reductase domain of MlnA from the macrolactin biosynthesis cluster from Bacillus amyloliquefaciens
ComponentsMlnA
KeywordsTRANSFERASE / polyketide / pks / enoyl reductase / trans-AT PKS / AT-less / TIM barrel
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
PfaD family protein / : / [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain / Malonyl CoA-acyl carrier protein transacylase, FabD-type / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesBacillus amyloliquefaciens subsp. plantarum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJakob, R.P. / Martin, S.F. / Herbst, D.A. / Maier, T.
CitationJournal: To Be Published
Title: The structural organization of trans-AT polyketide synthases: ketoacyl synthase and trans-acting enoyl reductase
Authors: Martin, S.F. / Jakob, R.P. / Herbst, D.A. / Maier, T.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MlnA
B: MlnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0584
Polymers106,1452
Non-polymers9132
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-39 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.170, 104.670, 216.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MlnA


Mass: 53072.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42) (bacteria)
Strain: DSM 23117 / BGSC 10A6 / FZB42 / Gene: mlnA, RBAM_014330 / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: A7Z470
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG3350, 0.2 M sodium malonate, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→108.05 Å / Num. obs: 23587 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 95.35 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.8
Reflection shellResolution: 2.8→2.92 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.7 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6J

2z6j


Resolution: 2.8→108.05 Å / Cor.coef. Fo:Fc: 0.8982 / Cor.coef. Fo:Fc free: 0.8992 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.396
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1213 5.14 %RANDOM
Rwork0.246 ---
obs0.2469 23587 99.69 %-
Displacement parametersBiso mean: 120.43 Å2
Baniso -1Baniso -2Baniso -3
1-5.3817 Å20 Å20 Å2
2---30.5483 Å20 Å2
3---25.1666 Å2
Refine analyzeLuzzati coordinate error obs: 0.849 Å
Refinement stepCycle: LAST / Resolution: 2.8→108.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13968 0 62 113 14143
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814205HARMONIC2
X-RAY DIFFRACTIONt_angle_deg125681HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3169SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2108HARMONIC5
X-RAY DIFFRACTIONt_it14205HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion17.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion924SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15053SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3396 145 5.14 %
Rwork0.3038 2677 -
all0.3058 2822 -
obs--99.69 %
Refinement TLS params.

T12: 0.152 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7191-1.4373-1.55930.56160.28272.48970.00950.27990.2273-0.0647-0.0895-0.2140.54420.54420.0799-0.2304-0.09790.304-0.1372-0.304-22.6118-15.559915.3598
24.6695-0.1441-1.43991.1531.49635.96990.19970.37960.5442-0.17780.1448-0.0213-0.4586-0.5442-0.3445-0.3040.0594-0.26810.152-0.2514-48.03720.849434.9605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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