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- PDB-3lzd: Crystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S ... -

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Basic information

Entry
Database: PDB / ID: 3lzd
TitleCrystal structure of Dph2 from Pyrococcus horikoshii with 4Fe-4S cluster
ComponentsDph2
KeywordsBIOSYNTHETIC PROTEIN / Diphthamide biosynthesis / radical SAM enzyme / gene triplication / iron-sulfur cluster
Function / homology
Function and homology information


S-adenosylmethionine catabolic process / 2-(3-amino-3-carboxypropyl)histidine synthase / 2-(3-amino-3-carboxypropyl)histidine synthase activity / protein histidyl modification to diphthamide / transferase activity, transferring alkyl or aryl (other than methyl) groups / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Diphthamide synthesis DPH1/DPH2 domain 1 / Diphthamide synthesis DPH1/DPH2 domain 2 / Diphthamide synthesis DPH1/DPH2 domain 3 / Diphthamide synthesis DPH1/DPH2 / Diphthamide synthesis Dph2, archaea / Diphthamide synthesis DHP1/DPH2, eukaryotes and archaea / Diphthamide synthesis DPH1/DPH2, domain 1 / Diphthamide synthesis DPH1/DPH2, domain 2 / Diphthamide synthesis DPH1/DPH2, domain 3 / Putative diphthamide synthesis protein ...Diphthamide synthesis DPH1/DPH2 domain 1 / Diphthamide synthesis DPH1/DPH2 domain 2 / Diphthamide synthesis DPH1/DPH2 domain 3 / Diphthamide synthesis DPH1/DPH2 / Diphthamide synthesis Dph2, archaea / Diphthamide synthesis DHP1/DPH2, eukaryotes and archaea / Diphthamide synthesis DPH1/DPH2, domain 1 / Diphthamide synthesis DPH1/DPH2, domain 2 / Diphthamide synthesis DPH1/DPH2, domain 3 / Putative diphthamide synthesis protein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / 2-(3-amino-3-carboxypropyl)histidine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsTorelli, A.T. / Zhang, Y. / Zhu, X. / Lee, M. / Dzikovski, B. / Koralewski, R.M. / Wang, E. / Freed, J. / Krebs, C. / Lin, H. / Ealick, S.E.
CitationJournal: Nature / Year: 2010
Title: Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme.
Authors: Zhang, Y. / Zhu, X. / Torelli, A.T. / Lee, M. / Dzikovski, B. / Koralewski, R.M. / Wang, E. / Freed, J. / Krebs, C. / Ealick, S.E. / Lin, H.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dph2
B: Dph2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0687
Polymers85,0772
Non-polymers9915
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.695, 80.525, 162.142
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 Dph2


Mass: 42538.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pDESTF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O58832
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 400, 0.06 M 2-(N-morpholino)ethanesulfonic acid, 0.12 M lithium sulfate, 3% ethylene glycol, pH 6.5, vapor diffusion, hanging drop, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 41255 / Num. obs: 41054 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Χ2: 0.916 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.41 / Num. unique all: 2192 / Rsym value: 0.241 / Χ2: 0.642 / % possible all: 66.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3LZC

3lzc


Resolution: 2.1→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2066 4.8 %Rfree selection matched (and extended) that of the starting model
Rwork0.204 ---
all0.204 41255 --
obs0.204 41054 94.5 %-
Solvent computationBsol: 55.931 Å2
Displacement parametersBiso max: 100.9 Å2 / Biso mean: 45.112 Å2 / Biso min: 18.56 Å2
Baniso -1Baniso -2Baniso -3
1-15.32 Å20 Å20 Å2
2--3.479 Å20 Å2
3----18.799 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5198 0 31 258 5487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.425
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2sf4.par
X-RAY DIFFRACTION3CNS_TOPPAR:water.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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