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- PDB-1im8: Crystal structure of YecO from Haemophilus influenzae (HI0319), a... -

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Basic information

Entry
Database: PDB / ID: 1im8
TitleCrystal structure of YecO from Haemophilus influenzae (HI0319), a methyltransferase with a bound S-adenosylhomocysteine
ComponentsYecO
KeywordsTRANSFERASE / methyltransferase / adenosylhomocysteine / structural genomics / hypothetical protein / Structure 2 Function Project / S2F
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / carboxyl- or carbamoyltransferase activity / tRNA wobble uridine modification / S-adenosyl-L-methionine binding
Similarity search - Function
Carboxy-S-adenosyl-L-methionine synthase / Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOSELENOCYSTEINE / Carboxy-S-adenosyl-L-methionine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae Rd (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLim, K. / Zhang, H. / Tempczyk, A. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2001
Title: Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine.
Authors: Lim, K. / Zhang, H. / Tempczyk, A. / Bonander, N. / Toedt, J. / Howard, A. / Eisenstein, E. / Herzberg, O.
History
DepositionMay 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / 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 / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YecO
B: YecO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9646
Polymers56,0302
Non-polymers9344
Water4,270237
1
A: YecO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4823
Polymers28,0151
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YecO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4823
Polymers28,0151
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: YecO
hetero molecules

A: YecO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9646
Polymers56,0302
Non-polymers9344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2650 Å2
ΔGint-38 kcal/mol
Surface area19430 Å2
MethodPISA
4
B: YecO
hetero molecules

B: YecO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9646
Polymers56,0302
Non-polymers9344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area2540 Å2
ΔGint-33 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.97, 74.97, 319.12
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein YecO / methyltransferase / HYPOTHETICAL PROTEIN HI0319


Mass: 28015.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI0319 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P43985, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SAI / S-ADENOSYL-L-HOMOSELENOCYSTEINE


Mass: 431.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5Se
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % saturated ammonium sulfate, 100mM NaHepes with protein solution (10mg/ml in 150mM NaCl, 10mM NaHepes, pH 8.0, 1mM DTT and 0.5mM EDTA) , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2150 mM1dropNaCl
310 mMsodium HEPES1drop
41 mMdithiothreitol1drop
50.5 mMEDTA1drop
620 %satammonium sulfate1reservoir
70.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9782, 0.9778, 0.9537
DetectorType: BRUKER / Detector: CCD / Date: Jul 3, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97821
20.97781
30.95371
ReflectionResolution: 2.2→20 Å / Num. all: 30031 / Num. obs: 30031 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.351 / % possible all: 74.6
Reflection
*PLUS
Num. obs: 51819 / % possible obs: 93.7 % / Num. measured all: 174537
Reflection shell
*PLUS
Highest resolution: 2.2 Å

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Processing

Software
NameClassification
SHELXmodel building
SOLVEphasing
MLPHAREphasing
DMmodel building
CNSrefinement
X-GENdata reduction
X-GENdata scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 1446 random
Rwork0.186 --
all-25465 -
obs-24873 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 54 237 3880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.192 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor obs: 0.253

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