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- PDB-9blq: X-ray crystal structure of Streptomyces cacaoi PolD with iron and... -

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Basic information

Entry
Database: PDB / ID: 9blq
TitleX-ray crystal structure of Streptomyces cacaoi PolD with iron and succinate bound
ComponentsPutative hydroxylase
KeywordsOXIDOREDUCTASE / iron / polyoxin / high-carbon sugar / nucleoside / 2-oxo-glutarate / ring-opening
Function / homology
Function and homology information


peptidyl-proline dioxygenase activity / regulation of translational termination / L-ascorbic acid binding / iron ion binding / cytoplasm
Similarity search - Function
: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / SUCCINIC ACID / Putative hydroxylase
Similarity search - Component
Biological speciesStreptomyces cacaoi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsCollazo-Perez, L.N. / Majer, S.H. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)119707 United States
CitationJournal: To Be Published
Title: Mechanism and evolutionary origin of the radical-mediated C-C bond cleavage in antifungal nucleotide biosynthesis
Authors: Du, Y. / Draelos, M. / Collazo-Perez, L.N. / Majer, S.H. / Boal, A.K. / Yokoyama, K.
History
DepositionMay 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative hydroxylase
B: Putative hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6746
Polymers53,3482
Non-polymers3264
Water1086
1
A: Putative hydroxylase
hetero molecules

A: Putative hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8888
Polymers53,3482
Non-polymers5406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area3740 Å2
ΔGint-72 kcal/mol
Surface area17860 Å2
MethodPISA
2
B: Putative hydroxylase
hetero molecules

B: Putative hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4604
Polymers53,3482
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2740 Å2
ΔGint-36 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.828, 58.828, 589.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

#1: Protein Putative hydroxylase / Putative hydroxylase


Mass: 26674.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cacaoi (bacteria) / Gene: polD / Production host: Escherichia coli (E. coli) / References: UniProt: C1IC31
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M Tris (pH 8.5), 0.2 M Li2SO4, 0.05 M sodium acetate, 15-20% (v/v) glycerol, and 22-28% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 17281 / % possible obs: 99 % / Redundancy: 8.2 % / Biso Wilson estimate: 45.33 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 2.75→2.82 Å / Num. unique obs: 984 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→49.31 Å / SU ML: 0.279 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 901 5.26 %RANDOM
Rwork0.2304 16214 --
obs0.2321 17115 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 15 6 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293360
X-RAY DIFFRACTIONf_angle_d0.64174583
X-RAY DIFFRACTIONf_chiral_restr0.0418508
X-RAY DIFFRACTIONf_plane_restr0.0044594
X-RAY DIFFRACTIONf_dihedral_angle_d18.86071198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.920.2971400.25842605X-RAY DIFFRACTION99.06
2.92-3.150.3521380.2652600X-RAY DIFFRACTION99.56
3.15-3.460.29881430.27292684X-RAY DIFFRACTION99.68
3.46-3.960.23551460.22072655X-RAY DIFFRACTION99.29
3.97-4.990.23771670.19032715X-RAY DIFFRACTION99.14
5-49.310.24691670.23432955X-RAY DIFFRACTION98.08
Refinement TLS params.Method: refined / Origin x: -20.3394300188 Å / Origin y: 33.7872277313 Å / Origin z: 25.6353244339 Å
111213212223313233
T0.418678734706 Å2-0.300806067939 Å20.0086880103203 Å2-0.0682188414833 Å2-0.0930167439058 Å2--0.221112902236 Å2
L0.245069013236 °2-0.03415935361 °2-0.0776412012652 °2-0.255191042495 °2-0.0363016548516 °2--0.14761256857 °2
S0.124507899401 Å °0.156833811507 Å °-0.252086755798 Å °-0.104396054843 Å °-0.0215158153503 Å °0.0206053452669 Å °0.131653882616 Å °-0.201088291362 Å °0.0783272978706 Å °
Refinement TLS groupSelection details: all

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