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- PDB-3fhm: Crystal structure of the CBS-domain containing protein ATU1752 fr... -

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Basic information

Entry
Database: PDB / ID: 3fhm
TitleCrystal structure of the CBS-domain containing protein ATU1752 from Agrobacterium tumefaciens
Componentsuncharacterized protein ATU1752
Keywordsstructural genomics / unknown function / NUCLEOTIDE-BINDING PROTEIN / CBS domain / prokaryotic / bound nucleotide / AMP / NADH / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


CBS domain-containing protein CBSX3, CBS domain / : / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / CBS domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSinger, A.U. / Xu, X. / Zhang, R. / Cui, H. / Kudritsdka, M. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the CBS-domain containing protein ATU1752 from Agrobacterium tumefaciens
Authors: Singer, A.U. / Brown, G. / Proudfoot, M. / Xu, X. / Dong, A. / Cui, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein ATU1752
B: uncharacterized protein ATU1752
C: uncharacterized protein ATU1752
D: uncharacterized protein ATU1752
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,81916
Polymers70,3844
Non-polymers4,43512
Water84747
1
A: uncharacterized protein ATU1752
D: uncharacterized protein ATU1752
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4098
Polymers35,1922
Non-polymers2,2176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-64 kcal/mol
Surface area12210 Å2
MethodPISA
2
B: uncharacterized protein ATU1752
C: uncharacterized protein ATU1752
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4098
Polymers35,1922
Non-polymers2,2176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-68 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.247, 58.075, 59.056
Angle α, β, γ (deg.)115.21, 106.15, 94.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A-5 - 211
2113B-5 - 211
3113C-5 - 211
4113D-5 - 211
DetailsDimer as represented by molecules B and C

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Components

#1: Protein
uncharacterized protein ATU1752


Mass: 17595.943 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: not cleaved with TEV.
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Strain: C58 / Gene: AGR_C_3216, Atu1752 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: A9CIP4
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris 8.0, 0.2 M LiSO4, 30% PEG 4K plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 16, 2008 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→30.37 Å / Num. all: 24264 / Num. obs: 19824 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.55
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.1 / Num. unique all: 143 / % possible all: 11.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
MrBUMPphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model of protein made from 3rc3 using MrBUMP

3rc3


Resolution: 2.7→30.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / SU B: 27.186 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.855 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26164 783 5.2 %RANDOM
Rwork0.19536 ---
obs0.19887 14238 91.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0.03 Å20.02 Å2
2--0.02 Å2-0.08 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 288 47 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2512.0355690
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90323.642151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.66115669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.071532
X-RAY DIFFRACTIONr_chiral_restr0.1460.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.21625
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22799
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A496tight positional0.080.05
2B496tight positional0.090.05
3C496tight positional0.080.05
4D496tight positional0.080.05
1A482loose positional0.625
2B482loose positional0.535
3C482loose positional0.645
4D482loose positional0.625
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.51 46 -
Rwork0.322 875 -
obs--76.62 %

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