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- PDB-5l1n: Pyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant -

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Basic information

Entry
Database: PDB / ID: 5l1n
TitlePyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant
ComponentsCoenzyme A disulfide reductase
KeywordsOXIDOREDUCTASE / sulfur metabolism half-sites reactivity
Function / homology
Function and homology information


CoA-disulfide reductase / CoA-disulfide reductase (NADPH) activity / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / protein disulfide isomerase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
Coenzyme A disulphide reductase / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain ...Coenzyme A disulphide reductase / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H coenzyme A polysulfide/persulfide reductase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSea, K. / Chen, B. / Crane III, E.J. / Sazinsky, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Research Corporation United States
CitationJournal: FEBS Open Bio / Year: 2018
Title: A broader active site inPyrococcus horikoshiiCoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry.
Authors: Sea, K. / Lee, J. / To, D. / Chen, B. / Sazinsky, M.H. / Crane, E.J.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme A disulfide reductase
B: Coenzyme A disulfide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7416
Polymers99,6352
Non-polymers3,1064
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.965, 191.965, 74.866
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 5 - 447 / Label seq-ID: 5 - 447

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.883665, 0.468108, 0.003331), (0.468098, -0.88367, 0.003409), (0.004539, -0.001453, -0.999989)-0.02681, 0.06825, -0.32613

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Components

#1: Protein Coenzyme A disulfide reductase / CoADR


Mass: 49817.340 Da / Num. of mol.: 2 / Mutation: Y65A, Y66A, Y67G, H367A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0572
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O58308, CoA-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 5-100 mM sodium acetate, pH 4.7, 50-100 mM ammonium acetate, 4-8% PEG 8000, and 0.01% sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.6→95.98 Å / Num. obs: 11879 / % possible obs: 99.4 % / Redundancy: 5.2 % / Rsym value: 0.041 / Net I/σ(I): 22.8
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FX9

4fx9


Resolution: 3.6→95.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 148.717 / SU ML: 1.539 / Cross valid method: THROUGHOUT / ESU R Free: 0.837 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28984 575 4.8 %RANDOM
Rwork0.24508 ---
obs0.24719 11302 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 180.276 Å2
Baniso -1Baniso -2Baniso -3
1--17.06 Å2-8.53 Å20 Å2
2---17.06 Å20 Å2
3---55.35 Å2
Refinement stepCycle: LAST / Resolution: 3.6→95.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6821 0 202 0 7023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197169
X-RAY DIFFRACTIONr_bond_other_d0.0110.026996
X-RAY DIFFRACTIONr_angle_refined_deg1.7562.0059743
X-RAY DIFFRACTIONr_angle_other_deg1.349316103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12923.986281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.015151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8091544
X-RAY DIFFRACTIONr_chiral_restr0.1380.21097
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217880
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.43117.4993537
X-RAY DIFFRACTIONr_mcbond_other7.4317.53536
X-RAY DIFFRACTIONr_mcangle_it12.56126.244416
X-RAY DIFFRACTIONr_mcangle_other12.5626.244417
X-RAY DIFFRACTIONr_scbond_it7.74218.6093632
X-RAY DIFFRACTIONr_scbond_other7.74118.613633
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.80527.6475328
X-RAY DIFFRACTIONr_long_range_B_refined20.65215863
X-RAY DIFFRACTIONr_long_range_B_other20.65115864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 4073 / Type: tight thermal / Rms dev position: 11.92 Å / Weight position: 0.5
LS refinement shellResolution: 3.601→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.496 42 -
Rwork0.459 846 -
obs--99.44 %

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