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- PDB-3fdi: Crystal structure of uncharacterized protein from Eubacterium ven... -

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Basic information

Entry
Database: PDB / ID: 3fdi
TitleCrystal structure of uncharacterized protein from Eubacterium ventriosum ATCC 27560.
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / Cytidylate kinase like protein / PSI / MCSG / PRK04182 class member / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyCytidylate kinase-like family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta / Cytidylate kinase-like family protein
Function and homology information
Biological speciesEubacterium ventriosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsNocek, B. / Keigher, L. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein from Eubacterium ventriosum ATCC 27560.
Authors: Nocek, B. / Keigher, L. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4088
Polymers46,9532
Non-polymers4556
Water1,13563
1
A: uncharacterized protein
B: uncharacterized protein
hetero molecules

A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,81716
Polymers93,9064
Non-polymers91012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9850 Å2
ΔGint-239 kcal/mol
Surface area31350 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-112 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.613, 114.932, 59.530
Angle α, β, γ (deg.)90.00, 128.06, 90.00
Int Tables number5
Space group name H-MC121
Detailsauthors state that the biological assembly is highly likely dimer.

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Components

#1: Protein uncharacterized protein


Mass: 23476.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium ventriosum (bacteria) / Strain: ATCC 27560 / Gene: EUBVEN_02315 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE(3) / References: UniProt: A5Z9C0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M (NH4)2SO4, Bis-Tris pH5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 22602 / Num. obs: 22354 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.73
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / Num. unique all: 1030 / % possible all: 89.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
Cootmodel building
MLPHAREphasing
CCP4model building
PHENIXmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
CCP4phasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 13.205 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.238 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24384 1147 5.1 %RANDOM
Rwork0.19751 ---
all0.202 22352 --
obs0.19969 21205 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.68 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å22.4 Å2
2---2.9 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 22 63 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222802
X-RAY DIFFRACTIONr_bond_other_d0.0020.021991
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9713744
X-RAY DIFFRACTIONr_angle_other_deg0.93134853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.7424.47132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3715569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1441519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.51683
X-RAY DIFFRACTIONr_mcbond_other0.2081.5690
X-RAY DIFFRACTIONr_mcangle_it1.63722716
X-RAY DIFFRACTIONr_scbond_it2.75731119
X-RAY DIFFRACTIONr_scangle_it4.3144.51028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 91 -
Rwork0.287 1386 -
obs--88.71 %
Refinement TLS params.Method: refined / Origin x: -1.5921 Å / Origin y: 99.4929 Å / Origin z: 22.3001 Å
111213212223313233
T0.066 Å20.0095 Å2-0.0017 Å2-0.0756 Å2-0.018 Å2--0.0474 Å2
L1.5845 °2-0.0195 °2-0.2556 °2-3.2462 °20.1231 °2--0.765 °2
S-0.0539 Å °-0.121 Å °0.1169 Å °0.1569 Å °0.1212 Å °-0.3255 Å °-0.0278 Å °-0.041 Å °-0.0673 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B199 - 229
2X-RAY DIFFRACTION1A199 - 230
3X-RAY DIFFRACTION1B2005 - 5001
4X-RAY DIFFRACTION1A2002 - 5001
5X-RAY DIFFRACTION1B2 - 196
6X-RAY DIFFRACTION1A3 - 196

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