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- PDB-7jua: Crystal structure of the second heterocyclization domain of yersi... -

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Basic information

Entry
Database: PDB / ID: 7jua
TitleCrystal structure of the second heterocyclization domain of yersiniabactin synthetase at 2.35 A resolution
ComponentsIrp2 protein
KeywordsBIOSYNTHETIC PROTEIN / heterocyclization domain
Function / homology
Function and homology information


toxin biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain ...Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsXia, Y. / Soule, J. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM123425-01 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: High-resolution structures of a siderophore-producing cyclization domain from Yersinia pestis offer a refined proposal of substrate binding.
Authors: Gnann, A.D. / Xia, Y. / Soule, J. / Barthelemy, C. / Mawani, J.S. / Musoke, S.N. / Castellano, B.M. / Brignole, E.J. / Frueh, D.P. / Dowling, D.P.
History
DepositionAug 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Irp2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9723
Polymers51,8291
Non-polymers1432
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-3 kcal/mol
Surface area18930 Å2
Unit cell
Length a, b, c (Å)89.271, 89.271, 140.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Irp2 protein / Ybt peptide synthetase HMWP2


Mass: 51828.766 Da / Num. of mol.: 1 / Fragment: heterocyclization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: irp2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z399
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 24196 / % possible obs: 99.3 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.043 / Rrim(I) all: 0.148 / Χ2: 0.911 / Net I/σ(I): 19.2 / Num. measured all: 285604
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.4312.10.8532.923490.8510.2520.890.67999.3
2.43-2.5312.20.65723610.9070.1940.6850.70599.4
2.53-2.6512.10.55123830.9360.1630.5750.72599.2
2.65-2.7912.10.40723800.9620.1210.4240.78199.6
2.79-2.96120.29323880.9770.0870.3060.83199.5
2.96-3.19120.19724040.9890.0590.2050.94999.5
3.19-3.5111.80.14124200.9940.0420.1471.12199.8
3.51-4.0211.60.10224400.9950.0310.1071.32899.8
4.02-5.0611.40.0724870.9980.0210.0731.09699.8
5.06-5010.70.05725840.9990.0180.060.90597.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JTJ

7jtj


Resolution: 2.35→22.33 Å / SU ML: 0.2719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1200 4.97 %transferred from MR model
Rwork0.1717 22958 --
obs0.1737 24158 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.33 Å2
Refinement stepCycle: LAST / Resolution: 2.35→22.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 9 227 3671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313593
X-RAY DIFFRACTIONf_angle_d0.56254921
X-RAY DIFFRACTIONf_chiral_restr0.0619535
X-RAY DIFFRACTIONf_plane_restr0.0039647
X-RAY DIFFRACTIONf_dihedral_angle_d17.19811314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.440.27291300.20682481X-RAY DIFFRACTION99.43
2.44-2.560.26181320.2032503X-RAY DIFFRACTION99.25
2.56-2.690.27411290.20642498X-RAY DIFFRACTION99.55
2.69-2.860.26731310.20012511X-RAY DIFFRACTION99.55
2.86-3.080.24891340.20052537X-RAY DIFFRACTION99.74
3.08-3.390.25371320.18492540X-RAY DIFFRACTION99.78
3.39-3.870.21350.16392563X-RAY DIFFRACTION99.96
3.88-4.870.14041340.13582605X-RAY DIFFRACTION99.89
4.87-22.330.18821430.15742720X-RAY DIFFRACTION99.13
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)
11.76869237013-0.3445301349580.4806089250131.06692437131-0.2835842694671.42320444118-0.0615554007716-0.219828443390.0265013308260.0290215940261-0.03482659656640.023883928304-0.109972217378-0.0309220802417-0.05685061245320.2353636519730.02330554622350.04208933147280.345659185971-0.002642215078720.309423646057-47.475431197124.5502019567-11.7610336131
20.55345984581-0.295208180597-0.1935151196050.200677773333-0.1597851137781.63321166340.169994897539-0.141851975177-0.142697795098-0.3169465138390.1994526203880.1970361514840.596421443357-0.01624847623830.3845163454480.313291383706-0.02012355488850.06726844944320.4130856196260.04235971018630.352678609097-54.72552410898.04856425668-12.5528874972
31.49906547893-0.05692136672910.306316364291.116171312610.2471461302651.694249011590.0664885259426-0.234276176639-0.1365462172150.1997342207640.03009478416220.02949423964810.211041562948-0.03317857286860.005285187431310.291024874559-0.03126359965940.01847983538570.2790925721730.01556365875140.229419661047-30.27432104616.56936227127-0.640571234177
40.7626066492010.3739734098930.3456441874890.647994430470.2708368597630.1760622063580.0595223373871-0.2369958371640.00502130799160.183106697648-0.125920400066-0.04390930477720.176752581915-0.595977741893-0.1170322278520.273009984459-0.03906142564310.08355374415240.492964961524-0.004312341061440.348289908121-37.30047675089.9202906768-1.05661957404
50.790938086420.43018007173-0.1064859416070.287929051895-0.259814567720.7346646208920.120807537155-0.0654298236570.04402245029140.06037866941990.00922107239380.0223741132257-0.0767661416756-0.014486619746-1.50311630321E-80.2749445993930.0111901118448-0.00662620087810.362883586404-0.02718334680370.297579900544-24.523980171916.4318018261-7.02472587425
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 1483 through 1641 )1483 - 16411 - 163
22chain 'A' and (resid 1642 through 1668 )1642 - 1668164 - 189
33chain 'A' and (resid 1669 through 1802 )1669 - 1802190 - 327
44chain 'A' and (resid 1803 through 1847 )1803 - 1847328 - 374
55chain 'A' and (resid 1848 through 1909 )1848 - 1909375 - 436

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