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- PDB-3lzc: Crystal structure of Dph2 from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 3lzc
TitleCrystal structure of Dph2 from Pyrococcus horikoshii
ComponentsDph2
KeywordsBIOSYNTHETIC PROTEIN / Diphthamide biosynthesis / radical SAM enzyme / gene triplication
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
2-(3-amino-3-carboxypropyl)histidine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.261 Å
AuthorsZhang, Y. / Zhu, X. / Torelli, A.T. / 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 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dph2
B: Dph2


Theoretical massNumber of molelcules
Total (without water)85,0772
Polymers85,0772
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-12 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.008, 82.598, 160.753
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): B834(DE3) / References: UniProt: O58832
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 8% PEG 4000, 0.1 M ammonium acetate, 0.05 M sodium citrate, 0.2 M KCl, 2% ethylene glycol, pH 5.3, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97922
SYNCHROTRONAPS 24-ID-E20.97918
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 21, 2008
ADSC QUANTUM 3152CCDAug 5, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979221
20.979181
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 24.38 / Number: 196000 / Rmerge(I) obs: 0.05 / Χ2: 1.31 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 51326 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385098.910.0231.1623.8
4.275.3810010.0451.6623.8
3.734.2710010.0421.9653.8
3.393.7310010.0471.4633.9
3.153.3910010.0691.3723.9
2.963.1510010.1131.2353.9
2.822.9610010.1661.0983.9
2.692.8210010.2331.073.9
2.592.6999.910.3211.0513.8
2.52.5998.510.4091.0373.7
ReflectionResolution: 2.25→50 Å / Num. all: 36442 / Num. obs: 36367 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Χ2: 1.047 / Net I/σ(I): 8.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1508 / Χ2: 0.51 / % possible all: 81.9

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Phasing

Phasing MAD setR cullis acentric: 1.52 / R cullis centric: 1 / Highest resolution: 3 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 13690 / Reflection centric: 2300
Phasing MAD set shell

ID: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricReflection acentricReflection centric
14.59-47.140.9210.20.17972
8.63-14.591.0510.20.2406168
6.13-8.631.3810.20.1984278
4.75-6.131.3610.10.11811368
3.88-4.751.2510.10.12901467
3.28-3.882.11004264564
2.84-3.2814.461003245383
2.5-2.84000000
Phasing MAD set site

Atom type symbol: Ano / B iso: 65 / Occupancy iso: 0

IDFract xFract yFract zOccupancy
10.7281.1950.9413.82
20.8950.9950.9213.577
30.5351.030.9933.282
40.8451.080.8112.987
51.1141.0760.9722.14
61.2220.830.8941.85
70.7631.3950.7821.616
81.130.7040.9061.394
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.59-47.140.2550.48701517972
8.63-14.590.3290.4650574406168
6.13-8.630.3770.48401262984278
4.75-6.130.3510.422021791811368
3.88-4.750.2990.347033682901467
3.28-3.880.2440.277048284264564
2.84-3.280.1540.172036283245383
2.5-2.8400000

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.261→40.188 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.771 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1848 5.08 %random
Rwork0.202 ---
all0.204 36442 --
obs0.204 36367 96.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.981 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 97.82 Å2 / Biso mean: 48.775 Å2 / Biso min: 26.41 Å2
Baniso -1Baniso -2Baniso -3
1-18.926 Å2-0 Å2-0 Å2
2---1.786 Å2-0 Å2
3----17.14 Å2
Refinement stepCycle: LAST / Resolution: 2.261→40.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 0 155 5425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085382
X-RAY DIFFRACTIONf_angle_d1.0357283
X-RAY DIFFRACTIONf_chiral_restr0.067820
X-RAY DIFFRACTIONf_plane_restr0.004938
X-RAY DIFFRACTIONf_dihedral_angle_d18.0331975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.261-2.3230.3061280.2592154228280
2.323-2.3910.2881040.2512487259192
2.391-2.4680.2731270.2462632275996
2.468-2.5560.3471610.252630279198
2.556-2.6590.2981520.2332683283599
2.659-2.780.331400.2322662280299
2.78-2.9260.3171380.2372698283699
2.926-3.1090.2861350.2412696283199
3.109-3.3490.2691670.222697286499
3.349-3.6860.2621310.2042743287499
3.686-4.2190.191400.1692770291099
4.219-5.3140.1571410.15627872928100
5.314-40.1950.2041840.1732880306499

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