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- PDB-3u4c: Crystal structure of YwfH, NADPH dependent reductase involved in ... -

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Basic information

Entry
Database: PDB / ID: 3u4c
TitleCrystal structure of YwfH, NADPH dependent reductase involved in Bacilysin biosynthesis
ComponentsBacilysin biosynthesis oxidoreductase ywfH
KeywordsOXIDOREDUCTASE / NADPH binding motif / Rossmann fold / SDR superfamily / Bacilysin biosynthesis
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / Oxidoreductases; Acting on the CH-CH group of donors; With 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
Chem-NDP / NADPH-dependent reductase BacG
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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 18, 2015Group: Experimental preparation
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Bacilysin biosynthesis oxidoreductase ywfH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2112
Polymers30,4661
Non-polymers7451
Water1,29772
1
A: Bacilysin biosynthesis oxidoreductase ywfH
hetero molecules

A: Bacilysin biosynthesis oxidoreductase ywfH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4224
Polymers60,9312
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area5310 Å2
ΔGint-31 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.301, 69.301, 206.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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Components

#1: Protein Bacilysin biosynthesis oxidoreductase ywfH


Mass: 30465.623 Da / Num. of mol.: 1
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: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 14, 2011 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→22.684 Å / Num. all: 20011 / Num. obs: 19411 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 17.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.7
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 3 / Num. unique all: 872 / % possible all: 90.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→22.684 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8264 / SU ML: 0.28 / σ(F): 2 / σ(I): 3 / Phase error: 23.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 949 5.16 %Random
Rwork0.2012 ---
all0.2033 20011 --
obs0.2033 18377 92.25 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.262 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 254.54 Å2 / Biso mean: 48.1474 Å2 / Biso min: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.6944 Å2-0 Å2-0 Å2
2--1.6944 Å20 Å2
3----3.3888 Å2
Refinement stepCycle: LAST / Resolution: 2.03→22.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 48 72 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082007
X-RAY DIFFRACTIONf_angle_d1.1232717
X-RAY DIFFRACTIONf_dihedral_angle_d16.063788
X-RAY DIFFRACTIONf_chiral_restr0.07312
X-RAY DIFFRACTIONf_plane_restr0.004350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.03-2.1370.32711280.2863234790
2.137-2.27080.40061020.349208879
2.2708-2.44590.29751460.2639241892
2.4459-2.69170.26611430.206261398
2.6917-3.08030.23241450.1901266899
3.0803-3.87780.23871380.1881237287
3.8778-22.68550.2021470.172292299
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)
10.5142-0.0051-0.02460.32440.34760.23550.1187-0.32581.0664-0.4041-0.0496-0.6763-0.61250.23770.01140.52370.01080.06080.1833-0.06940.3476-35.209126.478216.8885
21.5888-0.10240.42271.38051.11251.68470.0981-0.13010.45230.35350.12840.0021-0.32160.11560.00010.5087-0.01210.08530.2248-0.09930.2901-32.550227.798821.8178
30.55250.90340.01361.51030.59560.5921-0.0063-0.26980.10250.55440.2683-0.2847-0.1230.01980.00020.32370.07410.00790.2184-0.04430.2482-35.042410.466920.8879
40.7892-0.37920.27251.0644-1.13670.90450.62140.4417-0.5424-0.4822-0.3796-0.2241-0.18090.67910.07960.24150.10010.00580.2798-0.0770.3856-32.43810.18810.1236
5-0.0034-0.23210.10710.79180.1070.17950.2745-0.4350.2872-0.27540.032-0.11050.2575-0.275100.25590.02750.02360.19560.01210.2843-39.07996.418612.6174
60.20120.1468-0.21480.47040.39740.7928-0.6013-0.10550.18460.38110.5258-0.1433-0.09310.3985-0.00090.33130.088-0.0620.2894-0.08250.2878-26.495215.400810.79
70.18260.01860.2071-0.0694-0.02330.12130.0873-0.47030.5230.40580.4869-0.79-0.0191.21330.02050.38530.161-0.20040.8339-0.29890.5755-10.679111.06996.8131
80.49190.11720.25680.9068-0.59560.89090.2554-0.00730.073-0.08940.0296-0.0412-0.18960.0168-00.3185-0.00990.0580.2362-0.01140.2762-33.497317.35822.6604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain 'A' and (resseq 2:13)A2 - 13
2X-RAY DIFFRACTION2Chain 'A' and (resseq 14:80)A14 - 80
3X-RAY DIFFRACTION3Chain 'A' and (resseq 81:131)A81 - 131
4X-RAY DIFFRACTION4Chain 'A' and (resseq 132:151)A132 - 151
5X-RAY DIFFRACTION5Chain 'A' and (resseq 152:175)A152 - 175
6X-RAY DIFFRACTION6Chain 'A' and (resseq 176:194)A176 - 194
7X-RAY DIFFRACTION7Chain 'A' and (resseq 195:225)A195 - 225
8X-RAY DIFFRACTION8Chain 'A' and (resseq 226:259)A226 - 259

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