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- PDB-4tvy: Apo resorufin ligase -

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Basic information

Entry
Database: PDB / ID: 4tvy
TitleApo resorufin ligase
ComponentsLipoate-protein ligase A
KeywordsTRANSFERASE / E. coli LplA / computational enzyme design
Function / homology
Function and homology information


lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein lipoylation / ATP binding / cytosol / cytoplasm
Similarity search - Function
Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / Lipoyl protein ligase A/B catalytic domain / CO dehydrogenase flavoprotein, C-terminal domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Bira Bifunctional Protein; Domain 2 ...Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / Lipoyl protein ligase A/B catalytic domain / CO dehydrogenase flavoprotein, C-terminal domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Enolase-like; domain 1 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-(3,7-dihydroxy-10H-phenoxazin-2-yl)pentanamide / Lipoate-protein ligase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsGoldman, P.J. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Computational design of a red fluorophore ligase for site-specific protein labeling in living cells.
Authors: Liu, D.S. / Nivon, L.G. / Richter, F. / Goldman, P.J. / Deerinck, T.J. / Yao, J.Z. / Richardson, D. / Phipps, W.S. / Ye, A.Z. / Ellisman, M.H. / Drennan, C.L. / Baker, D. / Ting, A.Y.
History
DepositionJun 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoate-protein ligase A
B: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3356
Polymers76,0782
Non-polymers1,2574
Water2,900161
1
A: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6683
Polymers38,0391
Non-polymers6292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6683
Polymers38,0391
Non-polymers6292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.117, 89.951, 108.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipoate-protein ligase A / Lipoate--protein ligase


Mass: 38038.867 Da / Num. of mol.: 2 / Mutation: E20A, F147, H149G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lplA, yjjF, b4386, JW4349 / Production host: Escherichia coli (E. coli) / References: UniProt: P32099, EC: 2.7.7.63
#2: Chemical
ChemComp-37R / 5-(3,7-dihydroxy-10H-phenoxazin-2-yl)pentanamide


Mass: 314.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2 uL of 5.6 mg/mL resorufin ligase containing 1 mM resorufin sulfamoyladenosine, 1 mM Mg(OAc)2, and 1 mM dithiothreitol mixed with 2 uL of precipitant solution (11% PEG 20,000, 0.15 M MES: ...Details: 2 uL of 5.6 mg/mL resorufin ligase containing 1 mM resorufin sulfamoyladenosine, 1 mM Mg(OAc)2, and 1 mM dithiothreitol mixed with 2 uL of precipitant solution (11% PEG 20,000, 0.15 M MES:NaOH, pH 6.5). Red colored crystalline plates appeared after ~ 5 days. Crystals were looped and washed through a cryoprotection solution of 80% precipitant solution (12% PEG 20,000, 0.2 M MES:NaOH, pH 6.5) and 20% glycerol. Crystals were then cryocooled by direction submersion into liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→44.98 Å / Num. obs: 42531 / % possible obs: 99.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 38.63 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.25 / Rsym value: 0.541 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X2G

1x2g


Resolution: 2.151→44.976 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 2144 5.05 %
Rwork0.212 40353 -
obs0.2145 42497 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.9 Å2 / Biso mean: 45.3337 Å2 / Biso min: 24.04 Å2
Refinement stepCycle: final / Resolution: 2.151→44.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 138 161 5417
Biso mean--56.53 42.89 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065335
X-RAY DIFFRACTIONf_angle_d1.0337243
X-RAY DIFFRACTIONf_chiral_restr0.062779
X-RAY DIFFRACTIONf_plane_restr0.004948
X-RAY DIFFRACTIONf_dihedral_angle_d15.8551927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1509-2.20090.35911390.28822518265793
2.2009-2.2560.33261310.26792663279499
2.256-2.3170.30171380.265926842822100
2.317-2.38510.32941500.264526532803100
2.3851-2.46210.31811800.260126322812100
2.4621-2.55010.34281680.25812648281699
2.5501-2.65220.30481420.248527012843100
2.6522-2.77290.29491200.235726952815100
2.7729-2.91910.30111240.244127112835100
2.9191-3.10190.2951320.23672719285199
3.1019-3.34130.26461320.2212701283399
3.3413-3.67740.24941420.203727152857100
3.6774-4.20920.20561460.18722706285299
4.2092-5.30190.23161450.16932777292299
5.3019-44.98530.22961550.18892830298598

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