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- PDB-2p5f: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2p5f
TitleCrystal structure of PH0725 from Pyrococcus horikoshii OT3
Componentsdiphthine synthase
KeywordsTRANSFERASE / METHYLTRANSFERASE / 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 / DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsSugahara, M. / Yamamoto, H. / Kageyama, Y. / Taketa, M. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3
Authors: Sugahara, M. / Yamamoto, H. / Kageyama, Y. / Taketa, M. / Matsuura, Y. / Kunishima, N.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 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 / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,7313
Polymers59,3472
Non-polymers3841
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-27 kcal/mol
Surface area21240 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)119,4636
Polymers118,6944
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)104.773, 104.773, 139.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

DetailsBiological assembly is dimer in the asymmetric unit.

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Components

#1: Protein diphthine synthase / Diphthamide biosynthesis methyltransferase


Mass: 29673.482 Da / Num. of mol.: 2 / Mutation: A134M
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 18.015 Da / Num. of mol.: 235 / 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: 3.23 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.5
Details: 3.85M Sodium formate, 0.1M Sodium acetate, pH 5.5, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 27603 / Num. obs: 27603 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 51.302 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.095 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2667 / Rsym value: 0.585 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1WNG

1wng


Resolution: 2.5→14.99 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1371 -RANDOM
Rwork0.198 ---
obs0.198 27465 99.9 %-
all-27492 --
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 26 235 4439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.261 215 -
Rwork0.26 --
obs-4479 100 %

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