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- PDB-1vbf: Crystal structure of protein L-isoaspartate O-methyltransferase h... -

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Basic information

Entry
Database: PDB / ID: 1vbf
TitleCrystal structure of protein L-isoaspartate O-methyltransferase homologue from Sulfolobus tokodaii
Components231aa long hypothetical protein-L-isoaspartate O-methyltransferase
KeywordsTRANSFERASE / trimeric coiled coil assembly / inter-subunit disulfide bridge / protein repair enzyme
Function / homologyprotein-L-isoaspartate(D-aspartate) O-methyltransferase / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Protein-L-isoaspartate(D-aspartate) O-methyltransferase
Function and homology information
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsTanaka, Y. / Tsumoto, K. / Yasutake, Y. / Umetsu, M. / Yao, M. / Tanaka, I. / Fukada, H. / Kumagai, I.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: How Oligomerization Contributes to the Thermostability of an Archaeon Protein: PROTEIN L-ISOASPARTYL-O-METHYLTRANSFERASE FROM SULFOLOBUS TOKODAII
Authors: Tanaka, Y. / Tsumoto, K. / Yasutake, Y. / Umetsu, M. / Yao, M. / Fukada, H. / Tanaka, I. / Kumagai, I.
History
DepositionFeb 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
B: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
C: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
D: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)105,5034
Polymers105,5034
Non-polymers00
Water7,350408
1
A: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
B: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase

A: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
B: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase

A: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
B: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)158,2556
Polymers158,2556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
Buried area17630 Å2
ΔGint-92 kcal/mol
Surface area54620 Å2
MethodPISA, PQS
2
C: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
D: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase

C: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
D: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase

C: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase
D: 231aa long hypothetical protein-L-isoaspartate O-methyltransferase


Theoretical massNumber of molelcules
Total (without water)158,2556
Polymers158,2556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation21_554y,z+1/2,x-1/21
crystal symmetry operation29_554z+1/2,x,y-1/21
Buried area16320 Å2
ΔGint-103 kcal/mol
Surface area54390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)277.803, 277.803, 277.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
DetailsThe biological assembly is a hexamer. One hexamer can be generated from the chains A and B in the asymmetric unit by the operations: z, -x+1/2, -y+1/2 and -y+1/2, -z+1/2, x. Another can be generated from the chains C and D in the asymmetric unit by the operations: z+1/2, x, y-1/2 and y, z+1/2, x-1/2.

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Components

#1: Protein
231aa long hypothetical protein-L-isoaspartate O-methyltransferase / Protein L-isoaspartate O-methyltransferase


Mass: 26375.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: ST1123 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q972K9, protein-L-isoaspartate(D-aspartate) O-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 4.21 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: lithium sulfate, ammonium sulfate, citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→37.037 Å / Num. all: 43277 / Num. obs: 43276 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 22.9 % / Biso Wilson estimate: 57.2 Å2 / Rsym value: 0.082 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 22.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 6280 / Rsym value: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4281 -RANDOM
Rwork0.205 ---
all-42984 --
obs-42984 99.3 %-
Displacement parametersBiso mean: 49.8786 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 0 408 7576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009825
X-RAY DIFFRACTIONc_angle_deg1.65623
X-RAY DIFFRACTIONc_dihedral_angle_d24.42808
X-RAY DIFFRACTIONc_improper_angle_d0.95157
X-RAY DIFFRACTIONc_mcbond_it1.378
X-RAY DIFFRACTIONc_mcangle_it2.35
X-RAY DIFFRACTIONc_scbond_it2.25
X-RAY DIFFRACTIONc_scangle_it3.513
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.4008 411 -
Rwork0.3286 --
obs-3942 92.6 %

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