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- PDB-8xhp: The apo structure of SsBcmC -

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Basic information

Entry
Database: PDB / ID: 8xhp
TitleThe apo structure of SsBcmC
ComponentsFe/2OG dependent dioxygenase
KeywordsOXIDOREDUCTASE / Fe/2OG dependent dioxygenase / bicyclomycin / hydroxylation
Function / homology2-OXOGLUTARIC ACID / :
Function and homology information
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86000825296 Å
AuthorsWu, L. / Tang, G.L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Three distinct strategies lead to programmable aliphatic C-H oxidation in bicyclomycin biosynthesis.
Authors: Wu, L. / He, J.B. / Wei, W. / Pan, H.X. / Wang, X. / Yang, S. / Liang, Y. / Tang, G.L. / Zhou, J.
History
DepositionDec 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 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: Fe/2OG dependent dioxygenase
B: Fe/2OG dependent dioxygenase
C: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,64911
Polymers104,8593
Non-polymers7908
Water8,485471
1
A: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2474
Polymers34,9531
Non-polymers2943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1553
Polymers34,9531
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fe/2OG dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2474
Polymers34,9531
Non-polymers2943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.966, 74.233, 98.046
Angle α, β, γ (deg.)90.000, 104.134, 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

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Components

#1: Protein Fe/2OG dependent dioxygenase


Mass: 34952.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole pH6.5, 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride) and 10% PEG20000, 20%PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.86→19.772 Å / Num. obs: 75346 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.9139882543 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.072 / Net I/σ(I): 6.3
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4444 / CC1/2: 0.682 / Rpim(I) all: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSVersion February 5, 2021data reduction
XDSVersion February 5, 2021data scaling
PHASER1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V3O

7v3o


Resolution: 1.86000825296→19.7719294685 Å / SU ML: 0.220775477724 / Cross valid method: FREE R-VALUE / σ(F): 1.33784582786 / Phase error: 23.2818922412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231614889352 3849 5.10904336515 %
Rwork0.2053938082 71488 -
obs0.206766130415 75337 99.9761130648 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.0913021028 Å2
Refinement stepCycle: LAST / Resolution: 1.86000825296→19.7719294685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 45 471 6906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003522607141686604
X-RAY DIFFRACTIONf_angle_d0.7060061143648957
X-RAY DIFFRACTIONf_chiral_restr0.0451544150874937
X-RAY DIFFRACTIONf_plane_restr0.00427536437571217
X-RAY DIFFRACTIONf_dihedral_angle_d19.54328543143871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8600083-1.88350.3060576056411320.2748284864372590X-RAY DIFFRACTION100
1.8835-1.90830.3379727112631470.2651746634052661X-RAY DIFFRACTION99.9288256228
1.9083-1.93440.3138353761111370.2545268816972582X-RAY DIFFRACTION100
1.9344-1.9620.2449443249271510.2424828909792678X-RAY DIFFRACTION100
1.962-1.99130.2686024931441470.2342296268642605X-RAY DIFFRACTION99.9636759898
1.9913-2.02240.2638748814981330.2307014240352649X-RAY DIFFRACTION100
2.0224-2.05550.2502570303971340.2207470748342645X-RAY DIFFRACTION100
2.0555-2.09090.2489261845491530.211332910512621X-RAY DIFFRACTION100
2.0909-2.12890.2335324106891290.2055255294132657X-RAY DIFFRACTION100
2.1289-2.16980.2482983705891420.2127506780772636X-RAY DIFFRACTION100
2.1698-2.2140.2625397736521340.2090994850852648X-RAY DIFFRACTION100
2.214-2.26210.2376069892241230.1967585279592664X-RAY DIFFRACTION100
2.2621-2.31460.2612738089561450.2056540184012669X-RAY DIFFRACTION100
2.3146-2.37240.2265860495831350.2111382119842611X-RAY DIFFRACTION100
2.3724-2.43650.2298908423661190.202360558062668X-RAY DIFFRACTION99.9641319943
2.4365-2.5080.2531713754981500.2153036782292637X-RAY DIFFRACTION100
2.508-2.58880.2453329540031350.2179620076682644X-RAY DIFFRACTION100
2.5888-2.68110.2787313279441570.2212164207822644X-RAY DIFFRACTION100
2.6811-2.78820.2514432776781220.2156908396422649X-RAY DIFFRACTION100
2.7882-2.91470.2968998118431330.221296146882682X-RAY DIFFRACTION99.9290024849
2.9147-3.06780.2261708586911360.2106628265242682X-RAY DIFFRACTION99.9645264278
3.0678-3.25920.1851160928641520.2004364267962620X-RAY DIFFRACTION99.9279019466
3.2592-3.50960.2196745477431410.1970602629582669X-RAY DIFFRACTION100
3.5096-3.86040.204986961151550.1858486325952656X-RAY DIFFRACTION100
3.8604-4.41360.2010610861691380.183491599812685X-RAY DIFFRACTION100
4.4136-5.54030.204747260972040.1895466916972609X-RAY DIFFRACTION99.9644633973
5.5403-19.77190.2383702790181650.2012034679722727X-RAY DIFFRACTION99.8274076631

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