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- PDB-6bxk: Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S clust... -

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Basic information

Entry
Database: PDB / ID: 6bxk
TitleCrystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and MTA
Components2-(3-amino-3-carboxypropyl)histidine synthase
KeywordsBIOSYNTHETIC PROTEIN / DIPHTHAMIDE BIOSYNTHESIS / RADICAL SAM ENZYME
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
5'-DEOXY-5'-METHYLTHIOADENOSINE / IRON/SULFUR CLUSTER / 2-(3-amino-3-carboxypropyl)histidine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.347 Å
AuthorsTorelli, A.T. / Fenwick, M.K. / Zhang, Y. / Dong, M. / Kathiresan, V. / Carantoa, J.D. / Dzikovski, B. / Lancaster, K.M. / Freed, J.H. / Hoffman, B.M. ...Torelli, A.T. / Fenwick, M.K. / Zhang, Y. / Dong, M. / Kathiresan, V. / Carantoa, J.D. / Dzikovski, B. / Lancaster, K.M. / Freed, J.H. / Hoffman, B.M. / Lin, H. / Ealick, S.E.
CitationJournal: Science / Year: 2018
Title: Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Authors: Dong, M. / Kathiresan, V. / Fenwick, M.K. / Torelli, A.T. / Zhang, Y. / Caranto, J.D. / Dzikovski, B. / Sharma, A. / Lancaster, K.M. / Freed, J.H. / Ealick, S.E. / Hoffman, B.M. / Lin, H.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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_comp_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_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-(3-amino-3-carboxypropyl)histidine synthase
B: 2-(3-amino-3-carboxypropyl)histidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5678
Polymers85,0772
Non-polymers1,4906
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-98 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.509, 80.458, 161.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2-(3-amino-3-carboxypropyl)histidine synthase / Diphthamide biosynthesis protein Dph2 / S-adenosyl-L-methionine:L-histidine 3-amino-3-carboxypropyltransferase


Mass: 42538.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: dph2, PH1105 / Production host: Escherichia coli (E. coli)
References: UniProt: O58832, 2-(3-amino-3-carboxypropyl)histidine synthase
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 31-35% (v/v) PEG 400, either 0.1 M sodium citrate buffer pH 5.5 or MES buffer pH 6.5, 0.2 M Li2SO4 and 2% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 29510 / % possible obs: 94.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 53.56 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.031 / Net I/σ(I): 12 / Num. measured all: 130240
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.35-2.432.70.33823110.896175.3
2.43-2.533.50.32627080.89188.8
2.53-2.654.20.28329520.909196.3
2.65-2.794.70.22730500.98199
2.79-2.964.90.17230321.108199.2
2.96-3.194.80.12230421.185199.1
3.19-3.514.80.08330681.054198.4
3.51-4.024.80.06230621.073198.1
4.02-5.064.70.05530870.959197.3
5.06-504.50.0431981.081196.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3LZC

3lzc


Resolution: 2.347→40.48 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.79
RfactorNum. reflection% reflection
Rfree0.2504 1526 5.2 %
Rwork0.1803 --
obs0.184 29337 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.347→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 66 53 5303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075380
X-RAY DIFFRACTIONf_angle_d0.8477299
X-RAY DIFFRACTIONf_dihedral_angle_d18.2063217
X-RAY DIFFRACTIONf_chiral_restr0.051832
X-RAY DIFFRACTIONf_plane_restr0.005922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3475-2.42320.33211180.24351890X-RAY DIFFRACTION72
2.4232-2.50980.39211400.25352279X-RAY DIFFRACTION87
2.5098-2.61030.33571380.25452502X-RAY DIFFRACTION95
2.6103-2.72910.34921410.22892604X-RAY DIFFRACTION98
2.7291-2.87290.37451220.23112637X-RAY DIFFRACTION99
2.8729-3.05290.28521450.2172626X-RAY DIFFRACTION99
3.0529-3.28850.28021490.21552593X-RAY DIFFRACTION98
3.2885-3.61920.26251300.19322663X-RAY DIFFRACTION99
3.6192-4.14250.21951350.16442620X-RAY DIFFRACTION97
4.1425-5.21730.2121310.14292665X-RAY DIFFRACTION97
5.2173-40.4860.21711770.16042732X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.81191.47581.36818.00171.99868.10420.1216-0.3132-0.240.00310.00980.05760.2371-0.2743-0.1030.34340.0184-0.03010.54720.05230.2969.290121.620625.3338
22.2505-0.5946-0.73512.41940.21661.1285-0.1231-0.2908-0.0420.150.192-0.2654-0.09790.1654-0.0620.46060.014-0.03620.6584-0.0570.355735.32325.427238.8437
34.76830.3242.30491.1764-0.59384.0064-0.11060.14660.1328-0.3518-0.0033-0.2975-0.18480.54340.10850.6698-0.08710.07330.5098-0.05350.426130.105245.515918.3843
49.21136.29841.41184.3741.47693.8457-0.0428-0.87950.1835-0.0539-0.0461-0.186-0.3065-0.32520.07140.55740.1270.07340.60780.02110.362314.89129.088938.8815
55.60070.65643.03241.8309-0.61956.6599-0.347-0.34980.31680.03240.24870.0616-0.6942-0.21090.0830.87260.07220.00480.4543-0.04220.383110.398450.32046.2634
61.916-0.2598-0.70363.58871.2995.5047-0.00970.00210.0080.0668-0.012-0.0635-0.2013-0.00830.01180.4825-0.0395-0.0510.4520.04990.32884.660538.2134-19.4957
71.8019-0.1785-0.07673.5735-0.43428.8506-0.0050.0959-0.2292-0.30470.15020.14020.4301-0.186-0.13430.4161-0.0199-0.09210.43770.03990.3736.844517.85052.7714
81.1384-2.72050.29077.4101-1.79121.90960.17270.1110.048-0.5256-0.0913-0.07790.1643-0.2763-0.09490.5679-0.08320.02170.61320.03830.39125.733325.8605-0.6065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:93)
2X-RAY DIFFRACTION2(chain A and resid 94:211)
3X-RAY DIFFRACTION3(chain A and resid 212:323)
4X-RAY DIFFRACTION4(chain A and resid 324:341)
5X-RAY DIFFRACTION5(chain B and resid 1:93)
6X-RAY DIFFRACTION6(chain B and resid 94:209)
7X-RAY DIFFRACTION7(chain B and resid 210:271)
8X-RAY DIFFRACTION8(chain B and resid 272:341)

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