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- PDB-3cwo: A beta/alpha-barrel built by the combination of fragments from di... -

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Basic information

Entry
Database: PDB / ID: 3cwo
TitleA beta/alpha-barrel built by the combination of fragments from different folds
Componentsbeta/alpha-barrel protein based on 1THF and 1TMY
KeywordsDE NOVO PROTEIN / XRAY / CHEY / HISF / HALF BARREL
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBharat, T.A.M. / Eisenbeis, S. / Zeth, K. / Hocker, B.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: A beta alpha-barrel built by the combination of fragments from different folds.
Authors: Bharat, T.A. / Eisenbeis, S. / Zeth, K. / Hocker, B.
History
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.4Aug 30, 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
X: beta/alpha-barrel protein based on 1THF and 1TMY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1442
Polymers26,0481
Non-polymers961
Water50428
1
X: beta/alpha-barrel protein based on 1THF and 1TMY
hetero molecules

X: beta/alpha-barrel protein based on 1THF and 1TMY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2894
Polymers52,0962
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2250 Å2
ΔGint-45 kcal/mol
Surface area22470 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.840, 108.840, 80.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein beta/alpha-barrel protein based on 1THF and 1TMY


Mass: 26048.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-11 AND 34-103 FROM 1TMY, 103-253 FROM 1THF
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0C6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) at pH 6.5 with 1.6 M ammonium sulphate and 10% dioxane (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.071 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 3.1→36 Å / Num. all: 8681 / Num. obs: 7947 / % possible obs: 92.3 % / Observed criterion σ(I): 2.4 / Biso Wilson estimate: 96 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.5
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1386 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THF,1TMY

1thf

1tmy


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 43.299 / SU ML: 0.366 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.313 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25599 598 7 %RANDOM
Rwork0.22124 ---
all0.222 8681 --
obs0.22378 7947 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.258 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2---1.77 Å20 Å2
3---3.54 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 5 28 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221844
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9752488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1895235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00624.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.84215339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1691511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021338
X-RAY DIFFRACTIONr_nbd_refined0.2430.2911
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0030.21
X-RAY DIFFRACTIONr_mcbond_it0.4321.51192
X-RAY DIFFRACTIONr_mcangle_it0.77421875
X-RAY DIFFRACTIONr_scbond_it0.913708
X-RAY DIFFRACTIONr_scangle_it1.6534.5613
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 45 -
Rwork0.352 600 -
obs--100 %

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