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- PDB-9ubb: The structure of the AglA_K225E-Arg complex -

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Basic information

Entry
Database: PDB / ID: 9ubb
TitleThe structure of the AglA_K225E-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: 1.41 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5923
Polymers27,8011
Non-polymers7922
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-20 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.000, 73.310, 74.930
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 YqcI/YcgG family protein AglA


Mass: 27800.771 Da / Num. of mol.: 1 / Mutation: K225E
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
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: Sep 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.41→21.82 Å / Num. obs: 51662 / % possible obs: 99.98 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 13.04
Reflection shellResolution: 1.41→1.45 Å / Num. unique obs: 3617 / CC1/2: 0.564

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→21.82 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 2004 3.88 %
Rwork0.1762 --
obs0.1773 51661 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 0 373 2356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.017
X-RAY DIFFRACTIONf_dihedral_angle_d16.4742
X-RAY DIFFRACTIONf_chiral_restr0.081269
X-RAY DIFFRACTIONf_plane_restr0.011375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.26391390.26333478X-RAY DIFFRACTION100
1.45-1.480.24461440.23383498X-RAY DIFFRACTION100
1.48-1.530.28351450.22433494X-RAY DIFFRACTION100
1.53-1.580.21391350.19983501X-RAY DIFFRACTION100
1.58-1.630.19611480.18413515X-RAY DIFFRACTION100
1.63-1.70.24351350.17593522X-RAY DIFFRACTION100
1.7-1.780.20661420.16883539X-RAY DIFFRACTION100
1.78-1.870.2191430.16223516X-RAY DIFFRACTION100
1.87-1.990.17951460.16413525X-RAY DIFFRACTION100
1.99-2.140.19451440.16043552X-RAY DIFFRACTION100
2.14-2.360.20771420.16713548X-RAY DIFFRACTION100
2.36-2.70.21481460.1883586X-RAY DIFFRACTION100
2.7-3.390.22591450.18113620X-RAY DIFFRACTION100
3.4-100.16991500.15853763X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.69550.2412-0.311.9860.34281.55170.0862-0.21860.11730.2429-0.0597-0.0867-0.08620.0649-0.01810.1382-0.0158-0.01520.1099-0.02260.0936-4.18082.505720.7055
22.5737-0.47261.18941.95710.40231.64240.2098-0.1695-0.31530.2118-0.11860.19350.3629-0.1171-0.06170.1715-0.0256-0.00090.1027-0.00470.1278-11.6039-14.008914.2552
31.00970.3881-0.09331.66540.41082.00160.0666-0.0172-0.00220.03520.0005-0.0603-0.08430.111-0.06650.1066-0.012-0.01480.0991-0.01930.0991.65311.11712.1639
46.22120.98132.08741.68530.40041.7909-0.10810.53710.5436-0.22170.07510.0963-0.19080.13720.01270.1751-0.01440.00510.13860.02560.1607-2.2097.38210.5214
50.50050.23970.73081.73521.29752.51060.33930.7903-0.1183-0.0974-0.0067-0.2710.18360.4618-0.16960.11240.05630.01810.3283-0.01950.14437.9956-3.0378-6.5854
60.85290.76160.12690.70450.20920.38420.04850.0499-0.02070.0337-0.014-0.0679-0.022-0.011-0.03040.09840.0157-0.0130.1008-0.01680.0815-4.2084-5.96714.5784
72.9627-2.48840.22473.44460.54420.7537-0.13760.2128-0.60920.2582-0.04770.23390.174-0.18180.1930.1187-0.03880.01490.1078-0.0330.1478-12.6938-20.06463.5704
80.60120.57810.34531.5031-0.63321.1807-0.0423-0.0046-0.1566-0.1632-0.0648-0.06240.19990.16770.03710.1240.027-0.00340.14-0.00750.1078-13.2653-10.5266-3.5402
91.0976-0.29260.72511.1613-0.49822.0740.00710.19170.0058-0.0575-0.0393-0.054-0.0130.26940.0140.11070.0027-0.0160.1361-0.00770.0863-7.3907-4.2006-4.6013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 106 )
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 205 )
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 224 )
9X-RAY DIFFRACTION9chain 'A' and (resid 225 through 302 )

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