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- PDB-2eh2: Mutant V18M structure of PH0725 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2eh2
TitleMutant V18M 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, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, N-terminal domain / 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, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, N-terminal domain / 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: 2 Å
AuthorsShimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Mutant V18M structure of PH0725 from Pyrococcus horikoshii OT3
Authors: Shimizu, K. / Taketa, M. / Tanaka, Y. / Matsuura, Y. / Kunishima, N.
History
DepositionMar 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,84011
Polymers59,2912
Non-polymers1,5509
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-67 kcal/mol
Surface area21600 Å2
MethodPISA
2
A: diphthine synthase
B: diphthine synthase
hetero molecules

A: diphthine synthase
B: diphthine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,68122
Polymers118,5824
Non-polymers3,09918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
Buried area16740 Å2
ΔGint-147 kcal/mol
Surface area40160 Å2
MethodPISA, PQS
3
B: diphthine synthase
hetero molecules

B: diphthine synthase
hetero molecules

A: diphthine synthase
hetero molecules

A: diphthine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,68122
Polymers118,5824
Non-polymers3,09918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
crystal symmetry operation4_464y-1/2,-x+3/2,z-1/41
crystal symmetry operation5_556-x+1/2,y+1/2,-z+5/41
Buried area8590 Å2
ΔGint-110 kcal/mol
Surface area48320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.235, 104.235, 137.373
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: V18M
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 295 K / Method: microbach / pH: 6.5
Details: 1.8M Ammonium Sulfate, 0.1M MES, 0.01M Co Chloride, pH 6.5, 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 VII / Detector: IMAGE PLATE / Date: Oct 31, 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: 2→20 Å / Num. all: 51631 / Num. obs: 51631 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.056 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.362 / % possible all: 100

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Processing

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

1wng


Resolution: 2→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2599680.93 / 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
Rfree0.232 2565 5 %RANDOM
Rwork0.195 ---
obs0.195 51631 100 %-
all-51631 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8361 Å2 / ksol: 0.382326 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 94 463 4731
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 405 4.8 %
Rwork0.218 8021 -
obs--99.5 %
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
X-RAY DIFFRACTION5mes2.parammes2.top

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