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- PDB-1vce: Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 1vce
TitleCrystal structure of project ID PH0725 from Pyrococcus horikoshii OT3
Componentsdiphthine synthase
KeywordsTRANSFERASE / Structural Genomics / 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 / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKunishima, N. / Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3
Authors: Kunishima, N. / Shimizu, K.
History
DepositionMar 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)60,1743
Polymers59,7892
Non-polymers3841
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-25 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.721, 104.721, 138.672
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
11B-488-

HOH

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Components

#1: Protein diphthine synthase


Mass: 29894.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0725 / Plasmid: pET 11a / 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


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.: 478 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 291 K / Method: microbach / pH: 5.5
Details: 3.85M Na Formate, 0.1M Acetate, pH 5.5, microbach, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97938 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Feb 17, 2004 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 45662 / Num. obs: 45662 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 38.91 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 14 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.85 / Num. unique all: 4500 / Rsym value: 0.523 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→39.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2475497.89 / 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
Rfree0.253 2267 5 %RANDOM
Rwork0.218 ---
obs0.218 45662 100 %-
all-45662 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3075 Å2 / ksol: 0.370835 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 26 478 4676
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 368 4.9 %
Rwork0.278 7125 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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