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- PDB-2e4n: Mutant V251M structure of PH0725 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2e4n
TitleMutant V251M structure of PH0725 from Pyrococcus horikoshii OT3
Componentsdiphthine synthase
KeywordsTRANSFERASE / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation
Similarity search - Function
Diphthine synthase / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily ...Diphthine synthase / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Diphthine synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Mutant V251M structure of PH0725 from Pyrococcus horikoshii OT3
Authors: Shimizu, K. / Matsuura, Y. / Tanaka, Y. / Nakamoto, T. / Kunishima, N.
History
DepositionDec 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: diphthine synthase
B: diphthine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6984
Polymers59,2912
Non-polymers4072
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-37 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.199, 104.199, 138.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein diphthine synthase / / Diphthamide biosynthesis methyltransferase


Mass: 29645.432 Da / Num. of mol.: 2 / Mutation: V251M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58456, diphthine synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 295 K / Method: microbach / pH: 5.5
Details: 3.85M Na Formate, 0.1M Acetate, 1mM DTT, pH 5.5, Microbach, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 6, 2006 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 71276 / Num. obs: 71276 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.043 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.517 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WNG

1wng


Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2487738.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3613 5.1 %RANDOM
Rwork0.197 ---
obs0.197 71276 100 %-
all-71276 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.0271 Å2 / ksol: 0.375698 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 27 514 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 646 5.5 %
Rwork0.253 11065 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4sah.paramsah.top

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