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- PDB-9ubt: The structure of the AglA-Ampn-Arg complex -

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Basic information

Entry
Database: PDB / ID: 9ubt
TitleThe structure of the AglA-Ampn-Arg complex
ComponentsYqcI/YcgG family protein AglA
KeywordsBIOSYNTHETIC PROTEIN / hydroxylase
Function / homologyARGININE / PROTOPORPHYRIN IX CONTAINING FE / (aminomethyl)phosphonic acid
Function and homology information
Biological speciesStreptomyces monomycini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.596 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)31,7434
Polymers30,8401
Non-polymers9033
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-20 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.168, 72.221, 75.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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
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: Chemical ChemComp-PGL / (aminomethyl)phosphonic acid


Type: peptide-like / Mass: 111.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH6NO3P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
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 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.596→40.07 Å / Num. obs: 81136 / % possible obs: 99.74 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.63 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.16
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 6283 / CC1/2: 0.406

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.596→40.07 Å / SU ML: 0.1294 / Cross valid method: THROUGHOUT / Phase error: 17.1129
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.197 --RANDOM
Rwork0.1755 33857 --
obs-64912 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.95 Å2
Refinement stepCycle: LAST / Resolution: 1.596→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 60 274 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572078
X-RAY DIFFRACTIONf_angle_d0.96862850
X-RAY DIFFRACTIONf_chiral_restr0.0535273
X-RAY DIFFRACTIONf_plane_restr0.0093379
X-RAY DIFFRACTIONf_dihedral_angle_d18.9669748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.19441220.18232755X-RAY DIFFRACTION98.83
1.64-1.70.20571340.17732730X-RAY DIFFRACTION98.18
1.7-1.760.21231610.1812778X-RAY DIFFRACTION99.93
1.76-1.830.24591620.18652782X-RAY DIFFRACTION99.97
1.83-1.910.20881440.16962796X-RAY DIFFRACTION99.97
1.91-2.010.17971410.1582811X-RAY DIFFRACTION100
2.01-2.140.16771510.1592781X-RAY DIFFRACTION100
2.14-2.30.20671320.15882838X-RAY DIFFRACTION100
2.3-2.530.18321290.16972846X-RAY DIFFRACTION100
2.53-2.90.20491350.17512875X-RAY DIFFRACTION100
2.9-3.650.17541810.16352838X-RAY DIFFRACTION100
3.65-40.070.18041440.14813027X-RAY DIFFRACTION99.97
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)
10.117621093182-0.0135521820950.0227204664190.0554204574308-0.01082215288270.0731506911654-0.02619950593760.422142427739-0.00831252351336-0.2709390840870.0409903686210.2778953255960.162071461249-0.3743022751690.013606790540.1629641098630.00658308661336-0.03155811034430.1678942598550.01790393247610.178023664848-3.11154072961.55378953573-22.2269129713
20.610145599416-0.06699768643290.01328418238620.1519428147190.1259966890770.3991986467180.06784193159260.1241888779150.229114950647-0.131923767027-0.116871301197-0.157454641329-0.1567382821920.0558686556033-0.2244319069490.1190175731730.003190596889620.01205678453840.09828938915810.02106329469610.09229005182157.962161878554.03829415224-20.4556876305
30.2526456022280.1283252717470.1228662795980.395530299537-0.1451639624210.7415910277750.01621150453620.01002412028390.02838904299190.01195224667590.0128795720559-0.0329422284825-0.06276761122740.02457473509810.2525123261770.0980264981162-0.0119886917130.002358381087010.08131693024020.008149852412090.0800716014525.95897471828-3.85148485823-14.8229947522
40.125827725769-0.0346645556499-0.2717137913720.08566555146730.01669162060320.2927878214570.007891966950140.0692691194150.00961564608257-0.0519493284070.008526374998210.306132641243-0.0806555083114-0.1781641097670.01048376827530.1083973940020.0107785359204-0.007444423295330.1352488039570.02075679559820.143169076062-9.1773287702-1.61993212948-11.272311042
50.220587406996-0.1713320590330.09230563699760.100252257272-0.04669756672930.4032817380120.0665248811054-0.183614428972-0.131055441706-0.0439279750049-0.226865714804-0.435280222688-0.01665993527890.07834895683070.09021218409780.109793122491-0.015193317365-0.007946468441520.1056033917740.04286362169310.1530131519865.03722697817-0.356993906831-11.1242660234
60.2239424479-0.114211257219-0.02370392107540.249772347986-0.129513384020.1466627892590.0380145326119-0.08270291412730.3802438190980.0807453112203-0.0104566493024-0.116796087815-0.160302474851-0.0252605589615-0.0004145994714270.1913782477010.01144798518850.005530084073120.131534281606-0.02531874875930.153082915752.333757034897.38960687062-0.897754328632
70.4152697394470.308639016926-0.04810401198970.452159923956-0.1171076786810.2765215237650.0443119202265-0.1369115585740.07880488170810.05884893409880.01115666398030.0895136825081-0.0189133663481-0.0690962748660.03463228888760.1002563897680.002561855098640.005472633811650.1584941381170.009620401308580.118856782832-6.25974695763-3.367555874682.93158867449
80.71105190627-0.1877950126610.1416892214550.381924048648-0.1000821950350.5504603083230.0124934216556-0.00886032314677-0.0685740446797-0.0240525648334-0.0120361860018-0.03914787063020.01935487301480.03883546594460.3223079945220.0758775499612-0.00161690316731-0.0006545284826510.08548885383920.005671221469620.078299213160910.6874963452-10.4778979656-3.93930788457
90.758703690370.01485253122280.1265370513130.05359968295860.1564411577940.3931748655990.0130398549131-0.206102743376-0.02019585871340.0683874529051-0.0172302654839-0.0207691493414-0.00540401487436-0.02266048073360.01993055463450.1059615891450.00024783407621-0.007747638274130.10959474538-0.00339790759390.08100741983777.89926954601-5.753779898267.47283925254
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 13 )2 - 131 - 12
22chain 'A' and (resid 14 through 35 )14 - 3513 - 34
33chain 'A' and (resid 36 through 70 )36 - 7035 - 69
44chain 'A' and (resid 71 through 87 )71 - 8770 - 86
55chain 'A' and (resid 88 through 106 )88 - 10687 - 105
66chain 'A' and (resid 107 through 124 )107 - 124106 - 123
77chain 'A' and (resid 125 through 156 )125 - 156124 - 155
88chain 'A' and (resid 157 through 215 )157 - 215156 - 214
99chain 'A' and (resid 216 through 245 )216 - 245215 - 244

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