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- PDB-2ozv: Crystal structure of a predicted O-methyltransferase, protein Atu... -

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Basic information

Entry
Database: PDB / ID: 2ozv
TitleCrystal structure of a predicted O-methyltransferase, protein Atu636 from Agrobacterium tumefaciens.
ComponentsHypothetical protein Atu0636Hypothesis
KeywordsTRANSFERASE / structural genomics / Agrobacterium tumefaciens / predicted transferase / predicted O-methyltransferase / PFAM PF05175 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


methyltransferase activity / methylation / nucleic acid binding
Similarity search - Function
Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MTS domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCuff, M.E. / Xu, X. / Zheng, X. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a predicted O-methyltransferase, protein Atu636 from Agrobacterium tumefaciens.
Authors: Cuff, M.E. / Xu, X. / Zheng, X. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionFeb 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Atu0636
B: Hypothetical protein Atu0636


Theoretical massNumber of molelcules
Total (without water)57,3302
Polymers57,3302
Non-polymers00
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.544, 78.054, 62.261
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein Atu0636 / Hypothesis


Mass: 28664.871 Da / Num. of mol.: 2 / Fragment: Residues 31-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu0636 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21(DE3) / References: UniProt: Q8UHP4, UniProt: Q7D120*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Potassium thiocyanate, 30% PEG MME 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97906, 0.97923
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979061
20.979231
ReflectionResolution: 1.7→31.03 Å / Num. all: 48650 / Num. obs: 48650 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.396 / % possible all: 68.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.7→31.03 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.376 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.111
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21399 2489 5.1 %RANDOM
Rwork0.17767 ---
all0.17958 46159 --
obs0.17958 46159 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.014 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20.21 Å2
2---0.5 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 511 3673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213621
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9634951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3355501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93222.176170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91615613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0281548
X-RAY DIFFRACTIONr_chiral_restr0.1020.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022892
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21837
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22546
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2446
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2531.52404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50423741
X-RAY DIFFRACTIONr_scbond_it2.67831352
X-RAY DIFFRACTIONr_scangle_it3.9944.51202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 113 -
Rwork0.268 2303 -
obs--64.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9317-0.4318-0.36531.7511.19872.92090.0719-0.06660.08640.09240.0425-0.27150.02220.0723-0.1144-0.2987-0.0202-0.0208-0.35590.0121-0.282915.931515.35824.8753
21.22490.69391.41981.4410.94313.9-0.01180.0843-0.0021-0.08850.0771-0.01480.01330.0145-0.0653-0.3234-0.01070.042-0.311-0.0001-0.32677.9431.034-7.9324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 22923 - 221
2X-RAY DIFFRACTION2BB31 - 23123 - 223

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