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- PDB-9mri: X-ray crystal structure of Streptomyces cacaoi PolF bound to Zn(II) -

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Basic information

Entry
Database: PDB / ID: 9mri
TitleX-ray crystal structure of Streptomyces cacaoi PolF bound to Zn(II)
ComponentsMetal-bound non-heme metalloenzyme
KeywordsOXIDOREDUCTASE / zinc / iron / polyoximic acid / isoleucine / biosynthesis / oxidase / cyclization / heme-oxygenase-like diiron enzyme / BIOSYNTHETIC PROTEIN
Biological speciesStreptomyces cacaoi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.316 Å
AuthorsBlancas Cortez, J.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R35GM119707-09 United States
CitationJournal: To Be Published
Title: Radical-dependent azetidine biosynthesis by a diiron enzyme
Authors: Du, Y. / Thanapipatsiri, A. / Salas Sola, X.E. / Blancas Cortez, J.J. / Lin, C.Y. / Boal, A.K. / Krebs, C. / Bollinger, J.M. / Yokoyama, K.
History
DepositionJan 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-bound non-heme metalloenzyme
B: Metal-bound non-heme metalloenzyme
C: Metal-bound non-heme metalloenzyme
D: Metal-bound non-heme metalloenzyme
E: Metal-bound non-heme metalloenzyme
F: Metal-bound non-heme metalloenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,09014
Polymers193,5136
Non-polymers5778
Water6,287349
1
A: Metal-bound non-heme metalloenzyme
B: Metal-bound non-heme metalloenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6354
Polymers64,5042
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-91 kcal/mol
Surface area22280 Å2
MethodPISA
2
C: Metal-bound non-heme metalloenzyme
D: Metal-bound non-heme metalloenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7275
Polymers64,5042
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-91 kcal/mol
Surface area21770 Å2
MethodPISA
3
E: Metal-bound non-heme metalloenzyme
F: Metal-bound non-heme metalloenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7275
Polymers64,5042
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-92 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.586, 142.849, 161.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Metal-bound non-heme metalloenzyme


Mass: 32252.203 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cacaoi (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24.5% polyethylene glycol 4000, 0.2 M (NH4)2SO4, and 0.1 M Tri-sodium citrate, pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.316→33.706 Å / Num. obs: 87492 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.996 / Net I/σ(I): 7.1
Reflection shellResolution: 2.316→2.356 Å / Num. unique obs: 4290 / CC1/2: 0.362

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.316→33.706 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 875 1 %
Rwork0.2115 --
obs0.2118 87415 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.316→33.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12284 0 18 349 12651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.717
X-RAY DIFFRACTIONf_dihedral_angle_d15.1194478
X-RAY DIFFRACTIONf_chiral_restr0.0431905
X-RAY DIFFRACTIONf_plane_restr0.0052257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.460.32421430.303314184X-RAY DIFFRACTION100
2.46-2.650.32971450.272714300X-RAY DIFFRACTION100
2.65-2.920.28781450.249914305X-RAY DIFFRACTION100
2.92-3.340.28851450.225114396X-RAY DIFFRACTION100
3.34-4.210.21611460.185814465X-RAY DIFFRACTION100
4.21-33.7060.19741510.181214890X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.997 Å / Origin y: 5.8713 Å / Origin z: -57.8204 Å
111213212223313233
T0.2288 Å20.0355 Å2-0.0367 Å2-0.3524 Å20.0388 Å2--0.2589 Å2
L0.2711 °20.269 °2-0.331 °2-0.5349 °2-0.2821 °2--0.4954 °2
S0.0451 Å °0.0236 Å °-0.0098 Å °0.0329 Å °-0.0291 Å °0.0559 Å °-0.0621 Å °-0.0188 Å °-0.0146 Å °
Refinement TLS groupSelection details: all

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