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- PDB-9ub5: The structure of the AglA-Arg complex -

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Basic information

Entry
Database: PDB / ID: 9ub5
TitleThe structure of the AglA-Arg complex
ComponentsYqcI/YcgG family protein AglA
KeywordsBIOSYNTHETIC PROTEIN / hydroxylase
Function / homologyARGININE / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces monomycini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSun, Y. / Dou, C. / Yan, W. / Zhou, D. / Zhu, X. / Cheng, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32225001 China
National Natural Science Foundation of China (NSFC)32200114 China
CitationJournal: Adv Sci / Year: 2026
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
Revision 1.1Feb 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)31,6323
Polymers30,8401
Non-polymers7922
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-23 kcal/mol
Surface area11390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 76.460, 99.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

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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: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
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: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.83→36.65 Å / Num. obs: 26739 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 19.04
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 2611 / CC1/2: 0.888

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→36.65 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.462 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22061 1347 5 %RANDOM
Rwork0.16827 ---
obs0.1709 25392 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.83→36.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 55 202 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161854
X-RAY DIFFRACTIONr_angle_refined_deg2.3261.8542865
X-RAY DIFFRACTIONr_angle_other_deg0.8131.8044252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6315243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.608527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95610291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022625
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02557
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_it2.7872.148984
X-RAY DIFFRACTIONr_mcbond_other2.7822.15984
X-RAY DIFFRACTIONr_mcangle_it3.5013.8311223
X-RAY DIFFRACTIONr_mcangle_other3.5413.8361224
X-RAY DIFFRACTIONr_scbond_it4.4852.5971109
X-RAY DIFFRACTIONr_scbond_other4.4882.5991110
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3364.5441643
X-RAY DIFFRACTIONr_long_range_B_refined7.84823.22435
X-RAY DIFFRACTIONr_long_range_B_other7.83821.972390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 105 -
Rwork0.288 1835 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.9867 Å / Origin y: -18.0566 Å / Origin z: 2.4847 Å
111213212223313233
T0.032 Å2-0.033 Å20.0031 Å2-0.068 Å20.0064 Å2--0.008 Å2
L2.1024 °2-0.5425 °20.3306 °2-1.3325 °20.091 °2--2.4518 °2
S0.0827 Å °0.0226 Å °0.0501 Å °-0.0936 Å °-0.0289 Å °-0.0915 Å °0.0053 Å °0.0055 Å °-0.0537 Å °

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