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- PDB-8zhu: Structure of 3-amino-3-carboxyltransferase in complex with 5-thio... -

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Basic information

Entry
Database: PDB / ID: 8zhu
TitleStructure of 3-amino-3-carboxyltransferase in complex with 5-thioadenosine in the biosynthesis of nocardicins
ComponentsIsonocardicin synthase
KeywordsTRANSFERASE / 3-amino-3-carboxyltransferase / nocardicin / biosynthesis
Function / homologyisonocardicin synthase / Methyltransferase domain 25 / Methyltransferase domain / antibiotic biosynthetic process / transferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 5'-thioadenosine / Isonocardicin synthase
Function and homology information
Biological speciesNocardia uniformis subsp. tsuyamanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGao, Y. / Mori, T. / Awakawa, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of 3-amino-3-carboxyltransferase in complex with 5-thioadenosine in the biosynthesis of nocardicins
Authors: Gao, Y. / Mori, T. / Awakawa, T. / Abe, I.
History
DepositionMay 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 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: Isonocardicin synthase
B: Isonocardicin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6024
Polymers71,0362
Non-polymers5672
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-7 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.730, 94.317, 136.560
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 Isonocardicin synthase / Nocardicin 3-amino-3-carboxypropyltransferase


Mass: 35517.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia uniformis subsp. tsuyamanensis (bacteria)
Gene: nat, nocC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RAH6, isonocardicin synthase
#2: Chemical ChemComp-A4D / 5'-thioadenosine


Mass: 283.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 17% PEG 8000, 100 mM Tris-HCl pH 8.5, 200 mM MgCl2, 1 mM SAH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.16 Å / Num. obs: 25949 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.209 / Net I/σ(I): 10.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 15.8 % / Rmerge(I) obs: 1.551 / Mean I/σ(I) obs: 2 / Num. unique obs: 2699 / CC1/2: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.4→47.16 Å / SU ML: 0.2887 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2715 1999 7.73 %
Rwork0.2133 23863 -
obs0.2177 25862 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.86 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 0 95 4353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284347
X-RAY DIFFRACTIONf_angle_d0.63045921
X-RAY DIFFRACTIONf_chiral_restr0.0441670
X-RAY DIFFRACTIONf_plane_restr0.0062787
X-RAY DIFFRACTIONf_dihedral_angle_d5.1666643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.29511400.2941660X-RAY DIFFRACTION99.83
2.46-2.530.29341400.28111676X-RAY DIFFRACTION99.73
2.53-2.60.34011420.2661687X-RAY DIFFRACTION99.95
2.6-2.680.3181390.23831667X-RAY DIFFRACTION99.72
2.68-2.780.29981400.24871676X-RAY DIFFRACTION99.89
2.78-2.890.30551410.25211686X-RAY DIFFRACTION99.89
2.89-3.020.29981420.26981680X-RAY DIFFRACTION99.78
3.02-3.180.33021410.24371692X-RAY DIFFRACTION99.95
3.18-3.380.27051410.22191697X-RAY DIFFRACTION99.78
3.38-3.640.30221430.21441700X-RAY DIFFRACTION99.95
3.64-4.010.27011430.19031713X-RAY DIFFRACTION100
4.01-4.590.20981450.17121732X-RAY DIFFRACTION100
4.59-5.780.26361470.19241746X-RAY DIFFRACTION100
5.78-47.160.24251550.19241851X-RAY DIFFRACTION99.85
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)
14.00107597457-1.335124432421.459522791395.69662214738-2.067599980797.61412622733-0.170258439292-0.382126799880.7297416143780.235062059790.079465904492-0.63673480756-0.2022808968190.2514884316080.07460284347920.2268697289270.0349036111426-0.07142468598430.376947164808-0.06440745731880.4907902072999.7977105130417.701663378-26.5781379148
23.16209604361-2.274809971330.6952814730733.01496270172-1.522843133722.575700144-0.0634473167233-0.08806096272160.816619908353-0.0282582345828-0.0335107317146-0.737847946952-0.3712820491490.1091163377040.08868296518070.395630273345-0.004527087011990.01035641456870.333006016846-0.05699441070750.4830873472821.6729500812623.6229631659-36.0224405096
31.56396070801-1.70047882822-0.07008093352453.91622963666-0.2868313748042.090975962210.01003907907080.136762348566-0.0745725466549-0.130465777546-0.01826618145950.2339620900360.140378995458-0.357724646103-0.003641648499340.276056678194-0.0618442889591-0.02556487386640.3149255053860.02179968310930.287943202212-11.490787552529.5608782036-36.2336422494
43.85820915635-0.5700100915531.904156864566.0301223048-2.921190614318.075441097970.108585608777-0.425312205253-0.02147478766770.0180370714750.007278640410840.290715771640.379440525827-1.11818514872-0.1045450430990.247374117957-0.0777058225738-0.006186610625330.487370625287-0.03636894448590.362410924838-9.564000594557.60023058171-9.91789151127
52.50074478908-0.2559658082761.776525701472.6211969686-0.1740470533066.977124526350.15955967597-0.144563134723-0.3933562322180.19537024911-0.0298948551258-0.144933701711.190335202810.206003619911-0.1232476323870.5820058208540.0223641715785-0.07417620464890.3136011324250.01075387272720.3714943719827.616965032140.9834359927023.02812187125
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 91 )AA11 - 911 - 81
22chain 'A' and (resid 92 through 156 )AA92 - 15682 - 139
33chain 'A' and (resid 157 through 301 )AA157 - 301140 - 284
44chain 'B' and (resid 9 through 91 )BB9 - 911 - 81
55chain 'B' and (resid 92 through 301 )BB92 - 30182 - 287

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