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- PDB-6bxn: Crystal structure of Candidatus Methanoperedens nitroreducens Dph... -

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Basic information

Entry
Database: PDB / ID: 6bxn
TitleCrystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM
ComponentsDiphthamide biosynthesis enzyme Dph2
KeywordsBIOSYNTHETIC PROTEIN / DIPHTHAMIDE BIOSYNTHESIS / RADICAL SAM ENZYME
Function / homology
Function and homology information


2-(3-amino-3-carboxypropyl)histidine synthase / 2-(3-amino-3-carboxypropyl)histidine synthase activity / protein histidyl modification to diphthamide / 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 speciesCandidatus Methanoperedens nitroreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.079 Å
AuthorsFenwick, M.K. / Torelli, A.T. / Zhang, Y. / Dong, M. / Kathiresan, V. / Carantoa, J.D. / Dzikovski, B. / Lancaster, K.M. / Freed, J.H. / Hoffman, B.M. ...Fenwick, M.K. / Torelli, A.T. / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphthamide biosynthesis enzyme Dph2
B: Diphthamide biosynthesis enzyme Dph2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4196
Polymers72,9192
Non-polymers1,5004
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-64 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.476, 127.190, 142.462
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 Diphthamide biosynthesis enzyme Dph2


Mass: 36459.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanoperedens nitroreducens (archaea)
Gene: ANME2D_01646 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A062UZ78
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 65 mM HEPES, pH 6.5-7.0, and 18-25% (w/v) polyethylene glycol (PEG) 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 35318 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 31.85 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.047 / Rrim(I) all: 0.105 / Χ2: 1.123 / Net I/σ(I): 6.3 / Num. measured all: 159054
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.154.40.57934160.8420.2980.6540.68898.7
2.15-2.244.50.47435260.8960.2430.5360.72299.7
2.24-2.344.50.35834540.9360.1850.4050.73199.8
2.34-2.474.30.28435050.9540.1490.3230.78899.5
2.47-2.624.40.22135100.9790.1150.250.85298.7
2.62-2.824.90.16334840.9870.080.1820.95399.6
2.82-3.114.70.12435560.9910.0620.1391.10199.3
3.11-3.564.40.08235540.9940.0420.0931.44199.1
3.56-4.484.60.05635900.9970.0280.0631.78598.4
4.48-504.40.04837230.9980.0240.0542.07897

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Processing

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

3lzc


Resolution: 2.079→44.488 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.28
RfactorNum. reflection% reflection
Rfree0.2599 1679 4.77 %
Rwork0.2058 --
obs0.2084 35217 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.079→44.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 70 219 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084817
X-RAY DIFFRACTIONf_angle_d0.9266556
X-RAY DIFFRACTIONf_dihedral_angle_d16.012923
X-RAY DIFFRACTIONf_chiral_restr0.058760
X-RAY DIFFRACTIONf_plane_restr0.006836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0785-2.13970.36521400.2822697X-RAY DIFFRACTION98
2.1397-2.20880.32511320.25152762X-RAY DIFFRACTION99
2.2088-2.28770.33071490.24332745X-RAY DIFFRACTION100
2.2877-2.37930.26341300.21552783X-RAY DIFFRACTION100
2.3793-2.48760.26371460.21582761X-RAY DIFFRACTION99
2.4876-2.61870.29731330.22182785X-RAY DIFFRACTION98
2.6187-2.78280.28341330.21822776X-RAY DIFFRACTION100
2.7828-2.99760.28391270.21842792X-RAY DIFFRACTION99
2.9976-3.29910.26851620.21032795X-RAY DIFFRACTION99
3.2991-3.77630.23141440.18462784X-RAY DIFFRACTION98
3.7763-4.75690.22671380.17492884X-RAY DIFFRACTION99
4.7569-44.49790.23341450.20132974X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 11.883 Å / Origin y: 16.5934 Å / Origin z: 33.7036 Å
111213212223313233
T0.1415 Å2-0.0132 Å2-0.011 Å2-0.2345 Å20.0539 Å2--0.2503 Å2
L0.5564 °20.103 °20.043 °2-1.3318 °20.0504 °2--0.8271 °2
S0.0657 Å °-0.0078 Å °-0.028 Å °0.1187 Å °-0.0092 Å °-0.1063 Å °0.0326 Å °-0.1265 Å °-0.056 Å °
Refinement TLS groupSelection details: all

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