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

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Basic information

Entry
Database: PDB / ID: 6bxm
TitleCrystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved 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
ALPHA-AMINOBUTYRIC ACID / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 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: 2.252 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_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_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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)74,4217
Polymers72,9192
Non-polymers1,5025
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-63 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.887, 64.080, 158.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-ABA / ALPHA-AMINOBUTYRIC ACID / Α-Aminobutyric acid


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#5: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
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: 2.25→50 Å / Num. obs: 30482 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 31.03 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.05 / Rrim(I) all: 0.11 / Χ2: 1.01 / Net I/σ(I): 6.1 / Num. measured all: 138805
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.334.30.57930160.7970.3150.6620.86599.5
2.33-2.424.50.48429680.8390.2520.5470.85199.7
2.42-2.534.60.38230210.9060.1990.4330.86999.9
2.53-2.674.40.29130100.9330.1530.330.999.7
2.67-2.834.80.22930210.9610.1160.2580.92399.7
2.83-3.054.70.16530060.9740.0850.1870.95299.7
3.05-3.364.50.10830500.9880.0570.1221.09599.6
3.36-3.854.80.07230490.9940.0360.0811.20199.4
3.85-4.854.50.04630910.9970.0240.0521.1999.7
4.85-504.40.03732500.9990.0190.0421.21699

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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: 2.252→49.812 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.13
RfactorNum. reflection% reflection
Rfree0.227 1527 5.02 %
Rwork0.1748 --
obs0.1775 30423 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.252→49.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 70 200 5020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074962
X-RAY DIFFRACTIONf_angle_d0.9296757
X-RAY DIFFRACTIONf_dihedral_angle_d18.7722997
X-RAY DIFFRACTIONf_chiral_restr0.059789
X-RAY DIFFRACTIONf_plane_restr0.005859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2521-2.32480.27991120.21852534X-RAY DIFFRACTION96
2.3248-2.40790.27951360.20132604X-RAY DIFFRACTION100
2.4079-2.50430.29171370.19262586X-RAY DIFFRACTION100
2.5043-2.61830.25041480.19042593X-RAY DIFFRACTION100
2.6183-2.75630.23741320.18912593X-RAY DIFFRACTION100
2.7563-2.9290.2341260.19192642X-RAY DIFFRACTION100
2.929-3.15510.26311290.19612616X-RAY DIFFRACTION100
3.1551-3.47250.24721420.1822641X-RAY DIFFRACTION100
3.4725-3.97480.20421560.16342620X-RAY DIFFRACTION99
3.9748-5.00710.1941450.14242685X-RAY DIFFRACTION100
5.0071-49.82460.20471640.16562782X-RAY DIFFRACTION99

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