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- PDB-9ubs: The structure of the AglA_T220R-Arg complex -

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Basic information

Entry
Database: PDB / ID: 9ubs
TitleThe structure of the AglA_T220R-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: 1.49 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 3, 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)31,6323
Polymers30,8401
Non-polymers7922
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-21 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.974, 72.394, 75.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein YqcI/YcgG family protein AglA


Mass: 30840.201 Da / Num. of mol.: 1 / Mutation: T220R
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-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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
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: 1.49→36.2 Å / Num. obs: 80111 / % possible obs: 96.8 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 19.29
Reflection shellResolution: 1.49→1.53 Å / Num. unique obs: 5532 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→36.2 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 2002 4.75 %
Rwork0.1655 --
obs0.1667 64121 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 12 331 2308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.022
X-RAY DIFFRACTIONf_dihedral_angle_d17.782740
X-RAY DIFFRACTIONf_chiral_restr0.081269
X-RAY DIFFRACTIONf_plane_restr0.012373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.27041400.25362719X-RAY DIFFRACTION94
1.53-1.570.24311380.20562785X-RAY DIFFRACTION95
1.57-1.610.22561360.18492787X-RAY DIFFRACTION95
1.61-1.670.21321400.1712816X-RAY DIFFRACTION96
1.67-1.730.18991420.17172809X-RAY DIFFRACTION96
1.73-1.80.20021370.17492846X-RAY DIFFRACTION97
1.8-1.880.21771430.16682819X-RAY DIFFRACTION97
1.88-1.980.19331350.15822866X-RAY DIFFRACTION97
1.98-2.10.17981480.14922853X-RAY DIFFRACTION97
2.1-2.260.17031440.16022889X-RAY DIFFRACTION98
2.26-2.490.21151420.17072912X-RAY DIFFRACTION98
2.49-2.850.18481450.17372913X-RAY DIFFRACTION98
2.85-3.590.17381520.16442998X-RAY DIFFRACTION99
3.59-100.18251600.15043093X-RAY DIFFRACTION98
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)
12.62171.1048-0.41974.0038-0.64212.8882-0.02160.21690.1648-0.16370.17250.218-0.0461-0.1659-0.10870.15710.0164-0.02440.12670.02620.1249-0.1535.475-21.964
21.3197-0.64771.03342.5871-1.0412.28740.080.0844-0.0982-0.1079-0.0554-0.14030.17170.1184-0.01130.1239-0.00370.010.1083-0.00040.109410.453-9.151-16.474
31.262-0.1982-0.0391.901-0.37841.9335-0.0012-0.0392-0.0042-0.02490.00980.0244-0.1706-0.0609-0.02920.09160.0066-0.00660.07350.01920.0779-1.6362.159-12.003
48.5208-1.74671.52771.5784-0.35381.48670.0851-0.40920.54150.0559-0.0594-0.1201-0.1587-0.0595-0.03240.1970.00020.01630.1304-0.03040.15822.1667.431-0.777
52.50460.30130.04790.5907-0.04320.70950.093-0.21070.05160.0403-0.03080.0658-0.058-0.0343-0.05710.1151-0.0120.00320.13120.01340.12220.568-2.397-0.043
60.4361-0.1274-0.31342.3151-0.95680.70270.027-0.0368-0.19680.09690.01250.0589-0.00090.0175-0.04540.107-0.0082-0.01140.14580.02580.1607-0.306-11.684-4.515
75.03914.2570.346.5218-1.30841.752-0.0874-0.0308-0.40330.0091-0.0882-0.32630.030.28050.18810.12580.0199-0.00150.11950.03180.161112.812-19.956-3.586
81.6895-1.858-0.94822.24191.71492.7251-0.1976-0.1113-0.30220.2813-0.05360.04330.2506-0.05250.19120.1468-0.0403-0.0040.13510.00210.146913.44-9.9733.601
94.982-0.09280.28721.41820.1363.03250.0333-0.3593-0.02830.07330.01370.0486-0.0195-0.179-0.03850.1431-0.0067-0.01020.11430.00930.10978.443-1.9967.333
104.83033.09623.86471.98462.47723.0921-0.5352.05750.8489-0.2771.6512-0.74390.407-1.2943-1.09510.3861-0.0689-0.05040.9466-0.33490.71593.951-11.7680.017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:23 )A2 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:55 )A24 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:106 )A56 - 106
4X-RAY DIFFRACTION4( CHAIN A AND RESID 107:124 )A107 - 124
5X-RAY DIFFRACTION5( CHAIN A AND RESID 125:171 )A125 - 171
6X-RAY DIFFRACTION6( CHAIN A AND RESID 172:189 )A172 - 189
7X-RAY DIFFRACTION7( CHAIN A AND RESID 190:205 )A190 - 205
8X-RAY DIFFRACTION8( CHAIN A AND RESID 206:224 )A206 - 224
9X-RAY DIFFRACTION9( CHAIN A AND RESID 225:245 )A225 - 245
10X-RAY DIFFRACTION10( CHAIN A AND RESID 301:301 )A301

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