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- PDB-3u49: Crystal structure of YwfH, NADPH dependent reductase involved in ... -

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Basic information

Entry
Database: PDB / ID: 3u49
TitleCrystal structure of YwfH, NADPH dependent reductase involved in Bacilysin biosynthesis
ComponentsBacilysin biosynthesis oxidoreductase ywfH
KeywordsOXIDOREDUCTASE / NADPH binding motif / Rossmann fold / Short chain Dehydrogenase / reductase / SDR super family / Bacilysin biosynthesis
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / antibiotic biosynthetic process / NADP binding / cytoplasm
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADPH-dependent reductase BacG
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRajavel, M. / Gopal, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis
Authors: Rajavel, M. / Perinbam, K. / Gopal, B.
History
DepositionOct 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacilysin biosynthesis oxidoreductase ywfH
B: Bacilysin biosynthesis oxidoreductase ywfH
C: Bacilysin biosynthesis oxidoreductase ywfH
D: Bacilysin biosynthesis oxidoreductase ywfH


Theoretical massNumber of molelcules
Total (without water)121,8624
Polymers121,8624
Non-polymers00
Water7,386410
1
A: Bacilysin biosynthesis oxidoreductase ywfH
C: Bacilysin biosynthesis oxidoreductase ywfH


Theoretical massNumber of molelcules
Total (without water)60,9312
Polymers60,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-25 kcal/mol
Surface area21000 Å2
MethodPISA
2
B: Bacilysin biosynthesis oxidoreductase ywfH
D: Bacilysin biosynthesis oxidoreductase ywfH


Theoretical massNumber of molelcules
Total (without water)60,9312
Polymers60,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-25 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.850, 136.990, 66.700
Angle α, β, γ (deg.)90.00, 117.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bacilysin biosynthesis oxidoreductase ywfH


Mass: 30465.623 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU37680, ipa-86r, ywfH / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P39644
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 42.71 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.1M HEPES, 1.4M Tri-sodium citrate dihydrate, pH 7.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 24, 2010 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→68.5 Å / Num. all: 103248 / Num. obs: 102319 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.1 / Redundancy: 7.6 % / Biso Wilson estimate: 23.756 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.1 / Num. unique all: 15067 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→68.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.483 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4.1 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 5117 5 %RANDOM
Rwork0.18876 ---
all0.19044 103248 --
obs0.19044 97097 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.702 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.61 Å2
2---0.19 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati sigma a obs: 0.2454 Å
Refinement stepCycle: LAST / Resolution: 1.75→68.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 0 410 7929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227706
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.94510399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.78351004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7525.824340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.156151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2721533
X-RAY DIFFRACTIONr_chiral_restr0.0730.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215749
X-RAY DIFFRACTIONr_mcbond_it1.2361.54977
X-RAY DIFFRACTIONr_mcangle_it2.31227990
X-RAY DIFFRACTIONr_scbond_it2.88332729
X-RAY DIFFRACTIONr_scangle_it4.9044.52409
X-RAY DIFFRACTIONr_rigid_bond_restr1.35337706
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 361 -
Rwork0.248 7271 -
obs-15067 99.97 %
Refinement TLS params.

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)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0459-0.0122-0.01070.05810.01560.0355-0.00020.001-0.00410.0039-0.0005-0.00230.00340.00270.00070.0166-0.0012-0.00390.0044-0.00010.006724.4508-34.18552.6699
20.0289-0.00970.00860.0560.00180.06090.0070.0066-0.0009-0.0042-0.0030.00140.00470.0032-0.00390.01310.0015-0.00580.0069-0.00070.006711.7403-23.7379-24.6106
30.0663-0.0061-0.00930.05110.00670.0540.0006-0.00120.00130.00090.0008-0.0047-0.0009-0.0003-0.00140.0167-0.0001-0.00380.00350.00020.006422.2307-2.172213.3877
40.0415-0.02310.00990.0670.00880.0351-0.00060.0001-0.00280.0017-0.00090.0054-0.00060.00030.00150.01640.0006-0.00240.00610.00030.0055-0.6953.3025-8.1993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 44
2X-RAY DIFFRACTION1A45 - 54
3X-RAY DIFFRACTION1A55 - 166
4X-RAY DIFFRACTION1A167 - 258
5X-RAY DIFFRACTION2B3 - 44
6X-RAY DIFFRACTION2B45 - 54
7X-RAY DIFFRACTION2B55 - 166
8X-RAY DIFFRACTION2B167 - 258
9X-RAY DIFFRACTION3C3 - 44
10X-RAY DIFFRACTION3C45 - 54
11X-RAY DIFFRACTION3C55 - 166
12X-RAY DIFFRACTION3C167 - 258
13X-RAY DIFFRACTION4D3 - 44
14X-RAY DIFFRACTION4D45 - 54
15X-RAY DIFFRACTION4D55 - 166
16X-RAY DIFFRACTION4D167 - 258

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