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- PDB-4tvw: Resorufin ligase with bound resorufin-AMP analog -

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Basic information

Entry
Database: PDB / ID: 4tvw
TitleResorufin ligase with bound resorufin-AMP analog
ComponentsLipoate-protein ligase ALipoate–protein ligase
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 / 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 ...Lipoate-protein ligase A / Lipoate protein ligase, C-terminal / Bacterial lipoate protein ligase C-terminus / Lipoyltransferase/lipoate-protein ligase / 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 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-37P / Lipoate-protein ligase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.505 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 / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)154,7228
Polymers152,1554
Non-polymers2,5664
Water0
1
A: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6802
Polymers38,0391
Non-polymers6421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6802
Polymers38,0391
Non-polymers6421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6802
Polymers38,0391
Non-polymers6421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoate-protein ligase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6802
Polymers38,0391
Non-polymers6421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.354, 99.932, 107.284
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38038.867 Da / Num. of mol.: 4 / Fragment: UNP residues / Mutation: E20A, F147A, H149G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5a / Gene: lplA / Production host: Escherichia coli (E. coli) / References: UniProt: P32099, EC: 2.7.7.63
#2: Chemical
ChemComp-37P / 5'-O-{[5-(7-hydroxy-3-oxo-3H-phenoxazin-2-yl)pentanoyl]sulfamoyl}adenosine


Mass: 641.609 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H27N7O10S

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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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
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). Dark, and 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: Jul 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→49.98 Å / Num. obs: 21542 / % possible obs: 92 % / Redundancy: 2.8 % / Rsym value: 0.139 / Net I/σ(I): 7.8
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.333 / Rsym value: 0.265 / % possible all: 66.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 3.505→49.966 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.31 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 1049 5.12 %
Rwork0.2007 --
obs0.2032 20497 87.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.505→49.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10588 0 180 0 10768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311008
X-RAY DIFFRACTIONf_angle_d0.83814948
X-RAY DIFFRACTIONf_dihedral_angle_d15.2074020
X-RAY DIFFRACTIONf_chiral_restr0.0541628
X-RAY DIFFRACTIONf_plane_restr0.0031944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5052-3.68990.2474680.23971356X-RAY DIFFRACTION43
3.6899-3.9210.34861340.25312570X-RAY DIFFRACTION81
3.921-4.22360.31771550.21543123X-RAY DIFFRACTION98
4.2236-4.64840.2491720.18493102X-RAY DIFFRACTION98
4.6484-5.32040.19951410.17993091X-RAY DIFFRACTION97
5.3204-6.70060.24841970.22463097X-RAY DIFFRACTION98
6.7006-49.97110.19571820.17073109X-RAY DIFFRACTION96

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