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- PDB-9ub3: The structure of the apo-AglA from Streptomyces monomycini -

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Basic information

Entry
Database: PDB / ID: 9ub3
TitleThe structure of the apo-AglA from Streptomyces monomycini
ComponentsYqcI/YcgG family protein AglA
KeywordsBIOSYNTHETIC PROTEIN / hydroxylase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces monomycini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSun, Y. / Dou, C. / Yan, W. / Zhou, D. / Zhu, X. / Cheng, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32225001 China
National Natural Science Foundation of China (NSFC)32200114 China
CitationJournal: Adv Sci / Year: 2025
Title: A Dynamic Gate Enables Regioselective Hydroxylation of Free Arginine by a Non-Canonical Heme Enzyme.
Authors: Sun, Y. / Dou, C. / Yan, W. / Chen, P. / Zhang, L. / Zhou, D. / Zheng, Y. / Long, Z. / Li, S. / Xu, X. / Huang, Q. / Zhu, X. / Cheng, W.
History
DepositionApr 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YqcI/YcgG family protein AglA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4572
Polymers30,8401
Non-polymers6161
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-22 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.251, 77.251, 116.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YqcI/YcgG family protein AglA


Mass: 30840.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This protein corresponds to a novel sequence that is not available in UniProt at the time of biocuration. The sequence reference is GenBank Accession Number: URQ58546.1.
Source: (gene. exp.) Streptomyces monomycini (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Magnesium Chloride Hexahydrate, 0.1 M HEPES (pH 7.5) and 30% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.056→46.45 Å / Num. obs: 90468 / % possible obs: 99.92 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 4.35
Reflection shellResolution: 2.06→2.15 Å / Num. unique obs: 737 / CC1/2: 0.0175

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→46.45 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 9.171 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21391 1068 4.7 %RANDOM
Rwork0.1593 ---
obs0.16191 72421 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.06→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 43 63 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161810
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.8482817
X-RAY DIFFRACTIONr_angle_other_deg0.6841.7954155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.363525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88810282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022582
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02544
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.743.364971
X-RAY DIFFRACTIONr_mcbond_other8.7363.364971
X-RAY DIFFRACTIONr_mcangle_it12.2856.041212
X-RAY DIFFRACTIONr_mcangle_other12.2886.0411213
X-RAY DIFFRACTIONr_scbond_it11.2393.7671082
X-RAY DIFFRACTIONr_scbond_other11.2313.7671081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.8216.7171606
X-RAY DIFFRACTIONr_long_range_B_refined19.00732.842300
X-RAY DIFFRACTIONr_long_range_B_other18.97132.822296
X-RAY DIFFRACTIONr_rigid_bond_restr4.58233863
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.109 Å
RfactorNum. reflection% reflection
Rfree0.313 78 -
Rwork0.212 1551 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 14.2962 Å / Origin y: -19.3814 Å / Origin z: 4.4293 Å
111213212223313233
T0.0197 Å2-0.024 Å2-0.0088 Å2-0.0451 Å20.025 Å2--0.0183 Å2
L3.4626 °2-0.5573 °21.2019 °2-1.0976 °2-0.1775 °2--2.3195 °2
S-0.0154 Å °0.049 Å °0.0806 Å °-0.0751 Å °-0.013 Å °-0.0564 Å °-0.0958 Å °0.1264 Å °0.0283 Å °

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