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- PDB-8uyr: Manganese-substituted DitZ from Rhodococcus Rhodochrous -

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Basic information

Entry
Database: PDB / ID: 8uyr
TitleManganese-substituted DitZ from Rhodococcus Rhodochrous
ComponentsDitZ
KeywordsOXIDOREDUCTASE / Monooxygenase / diterpenoid / diiron
Function / homology:
Function and homology information
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLiu, C. / Chen, S. / Rittle, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A Widespread, Diiron-dependent Diterpenoid Hydroxylase
Authors: Chen, S. / Liu, C. / Rittle, J.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DitZ
B: DitZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,50014
Polymers94,6112
Non-polymers88912
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-42 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.744, 92.693, 145.122
Angle α, β, γ (deg.)90.000, 99.944, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21A-770-

HOH

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Components

#1: Protein DitZ


Mass: 47305.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M MgCl2, 0.08 M Tris pH 8.5, 16.8% PEG 4000, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→39.44 Å / Num. obs: 68822 / % possible obs: 92.44 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.74 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.83
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 5.5 % / Num. unique obs: 4565 / CC1/2: 0.625 / % possible all: 61.37

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→39.44 Å / SU ML: 0.1749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9557 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1931 2033 2.95 %
Rwork0.1615 66789 -
obs0.1625 68822 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.01 Å2
Refinement stepCycle: LAST / Resolution: 1.82→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 47 671 7347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836909
X-RAY DIFFRACTIONf_angle_d0.98319401
X-RAY DIFFRACTIONf_chiral_restr0.06081002
X-RAY DIFFRACTIONf_plane_restr0.00651225
X-RAY DIFFRACTIONf_dihedral_angle_d15.01092521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.2837820.2482831X-RAY DIFFRACTION59.05
1.86-1.910.25191130.23143259X-RAY DIFFRACTION68.34
1.91-1.960.26511210.2123864X-RAY DIFFRACTION80.65
1.96-2.020.241300.20044593X-RAY DIFFRACTION95.09
2.02-2.080.23541470.18144744X-RAY DIFFRACTION98.49
2.08-2.160.20991360.17774730X-RAY DIFFRACTION98.52
2.16-2.240.21851390.17164739X-RAY DIFFRACTION98.72
2.24-2.350.19971400.16314695X-RAY DIFFRACTION97.28
2.35-2.470.22591440.16524725X-RAY DIFFRACTION98.82
2.47-2.620.20781450.16644727X-RAY DIFFRACTION99.04
2.62-2.830.19221480.16794716X-RAY DIFFRACTION97.53
2.83-3.110.1651480.16114774X-RAY DIFFRACTION98.86
3.11-3.560.17931410.15254795X-RAY DIFFRACTION99.1
3.56-4.490.15611480.1284755X-RAY DIFFRACTION98.34
4.49-39.440.17231510.14614842X-RAY DIFFRACTION98.46

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