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- PDB-2wr8: Structure of Pyrococcus horikoshii SAM hydroxide adenosyltransfer... -

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Basic information

Entry
Database: PDB / ID: 2wr8
TitleStructure of Pyrococcus horikoshii SAM hydroxide adenosyltransferase in complex with SAH
ComponentsPUTATIVE UNCHARACTERIZED PROTEIN PH0463
KeywordsTRANSFERASE / SAM / SAM HYDROXIDE ADENOSYLTRANSFERASE (DUF-62) / SN2 / WATER ACTIVATION
Function / homology
Function and homology information


(R)-S-adenosyl-L-methionine hydrolase (adenosine-forming) / hydrolase activity
Similarity search - Function
Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 ...Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / (R)-S-adenosyl-L-methionine hydrolase
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMcMahon, S.A. / Deng, H. / O'Hagan, D. / Johnson, K.A. / Naismith, J.H.
CitationJournal: Chembiochem / Year: 2009
Title: Mechanistic Insights Into Water Activation in Sam Hydroxide Adenosyltransferase (Duf-62).
Authors: Deng, H. / Mcmahon, S.A. / Eustaquio, A.S. / Moore, B.S. / Naismith, J.H. / O'Hagan, D.
History
DepositionAug 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE UNCHARACTERIZED PROTEIN PH0463
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3192
Polymers28,9341
Non-polymers3841
Water2,072115
1
A: PUTATIVE UNCHARACTERIZED PROTEIN PH0463
hetero molecules

A: PUTATIVE UNCHARACTERIZED PROTEIN PH0463
hetero molecules

A: PUTATIVE UNCHARACTERIZED PROTEIN PH0463
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9576
Polymers86,8033
Non-polymers1,1533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area8720 Å2
ΔGint-53.6 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.561, 65.561, 142.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2009-

HOH

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Components

#1: Protein PUTATIVE UNCHARACTERIZED PROTEIN PH0463 / SAM HYDROXIDE ADENOSYLTRANSFERASE


Mass: 28934.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: OT3 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 C43(DE3) / References: UniProt: O58212
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1 Å3/Da / Density % sol: 41.6 % / Description: NONE
Crystal growpH: 7 / Details: 19.83% PEG 6000, 0.26M KCL, 0.1M MOPS PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2008 / Details: TORODIAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 22346 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.4
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WU8

1wu8


Resolution: 1.77→52.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.293 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21739 1137 5.1 %RANDOM
Rwork0.16796 ---
obs0.17039 21127 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.439 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.78 Å20 Å2
2---1.57 Å20 Å2
3---2.35 Å2
Refinement stepCycle: LAST / Resolution: 1.77→52.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 26 115 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222109
X-RAY DIFFRACTIONr_bond_other_d0.0020.021440
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9952861
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0013506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94623.93389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4361513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_nbd_refined0.2120.2380
X-RAY DIFFRACTIONr_nbd_other0.2110.21460
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21007
X-RAY DIFFRACTIONr_nbtor_other0.1090.21095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1461.51675
X-RAY DIFFRACTIONr_mcbond_other0.2611.5527
X-RAY DIFFRACTIONr_mcangle_it1.30122095
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3313947
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1174.5765
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.769→1.815 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 85 -
Rwork0.193 1550 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 14.189 Å / Origin y: -27.603 Å / Origin z: 2.207 Å
111213212223313233
T-0.1307 Å2-0.0115 Å20.0349 Å2--0.1255 Å2-0.0181 Å2---0.2018 Å2
L1.8014 °20.162 °20.5215 °2-1.9108 °2-0.2617 °2--0.8716 °2
S-0.0125 Å °0.1771 Å °0.1009 Å °-0.048 Å °0.0446 Å °-0.2498 Å °-0.0885 Å °0.1196 Å °-0.0321 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 162
2X-RAY DIFFRACTION1A163 - 256

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