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

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Basic information

Entry
Database: PDB / ID: 6bxl
TitleCrystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM
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 / 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
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 2-(3-amino-3-carboxypropyl)histidine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.301 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)86,5776
Polymers85,0772
Non-polymers1,5004
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-56 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.035, 80.904, 161.058
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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
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: Oct 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 33136 / % possible obs: 97.8 % / Redundancy: 4 % / Biso Wilson estimate: 46.11 Å2 / Rmerge(I) obs: 0.055 / Χ2: 0.989 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.3540.36119460.949188.1
2.35-2.4140.33720910.876194.5
2.41-2.484.10.28321800.906196.6
2.48-2.554.10.24421950.903199.9
2.55-2.634.10.20322110.892199.8
2.63-2.7340.16722350.994199.9
2.73-2.844.10.13622280.987199.9
2.84-2.974.10.10822261.086199.8
2.97-3.124.10.08322381.098199.4
3.12-3.3240.06522401.029199.5
3.32-3.5740.05622371.03199.1
3.57-3.9340.05222411.092198.9
3.93-4.53.90.04722631.043198
4.5-5.673.80.03722520.984198
5.67-503.90.02523530.958195.4

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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: 2.301→46.544 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.06
RfactorNum. reflection% reflection
Rfree0.2491 1684 5.11 %
Rwork0.188 --
obs0.1912 32972 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.301→46.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 70 69 5358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075456
X-RAY DIFFRACTIONf_angle_d0.8317399
X-RAY DIFFRACTIONf_dihedral_angle_d18.9623285
X-RAY DIFFRACTIONf_chiral_restr0.051836
X-RAY DIFFRACTIONf_plane_restr0.005939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3014-2.36920.40121050.2852299X-RAY DIFFRACTION86
2.3692-2.44560.27211390.29162493X-RAY DIFFRACTION95
2.4456-2.5330.40581530.2752567X-RAY DIFFRACTION98
2.533-2.63440.37491520.26782604X-RAY DIFFRACTION99
2.6344-2.75430.38431310.25712644X-RAY DIFFRACTION99
2.7543-2.89950.3671340.2392650X-RAY DIFFRACTION99
2.8995-3.08120.28981440.23242629X-RAY DIFFRACTION100
3.0812-3.3190.29431570.23082655X-RAY DIFFRACTION99
3.319-3.65290.27381200.18922668X-RAY DIFFRACTION99
3.6529-4.18120.21561410.16072651X-RAY DIFFRACTION98
4.1812-5.26670.17391340.13412684X-RAY DIFFRACTION98
5.2667-46.55320.19381740.1562744X-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)
17.67561.8284-2.40718.1348-0.6116.41060.205-0.7856-0.58191.09330.09930.3410.899-0.3548-0.28160.542-0.0497-0.06680.55140.12080.34558.175715.79525.5858
22.5435-0.34061.24351.1912-0.11362.6351-0.1387-0.11720.05840.4540.1585-0.1913-0.32320.2019-0.02650.76160.0179-0.0420.4593-0.03160.314328.849726.273734.6693
34.4819-0.02862.37661.2168-0.47661.7675-0.29140.06310.2272-0.19170.0044-0.3081-0.88690.7390.29531.1676-0.2242-0.0030.59870.00070.448130.866745.671517.7438
47.20796.31052.25739.38362.37060.7535-0.03-0.40760.33210.5844-0.2616-0.0615-0.3269-0.41540.26690.82210.13720.05770.5130.01330.315818.962331.785436.7691
51.53340.23722.05621.29470.61031.8426-0.4171-0.27110.40810.30550.2989-0.038-1.371-0.28130.07631.36090.0928-0.06030.496-0.00030.51411.024649.77752.5003
63.9305-0.8892-0.83096.5796-0.68454.3341-0.1272-0.0833-0.1102-0.0420.34490.1075-0.1201-0.2239-0.210.6098-0.0594-0.00050.39560.03430.27053.474837.134-19.0865
72.3347-0.22981.18182.4548-0.55138.85750.1160.0384-0.3306-0.44790.12850.05770.5043-0.0204-0.23580.4391-0.0283-0.06370.31050.06740.36228.75218.14333.5485
81.2668-3.32520.49238.3699-1.9782.66580.38250.13550.1319-0.3545-0.2052-0.0993-0.1518-0.4753-0.17820.76150.01050.00570.61040.05910.41443.091128.1001-3.2601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 3:48
2X-RAY DIFFRACTION2chain A and resseq 49:210
3X-RAY DIFFRACTION3chain A and resseq 211:319
4X-RAY DIFFRACTION4chain A and resseq 320:341
5X-RAY DIFFRACTION5chain B and resseq 1:108
6X-RAY DIFFRACTION6chain B and resseq 109:208
7X-RAY DIFFRACTION7chain B and resseq 209:286
8X-RAY DIFFRACTION8chain B and resseq 287:341

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