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- PDB-6n2b: The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapi... -

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Basic information

Entry
Database: PDB / ID: 6n2b
TitleThe Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain
ComponentsTapirin
KeywordsCELL ADHESION / BETA-HELIX / cellulose binding
Function / homologymetal ion binding / membrane / Type 4 fimbrial biogenesis protein PilX N-terminal domain-containing protein
Function and homology information
Biological speciesCaldicellulosiruptor kristjanssonii
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Appl. Environ. Microbiol. / Year: 2019
Title: Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely ThermophilicCaldicellulosiruptorSpecies.
Authors: Lee, L.L. / Hart, W.S. / Lunin, V.V. / Alahuhta, M. / Bomble, Y.J. / Himmel, M.E. / Blumer-Schuette, S.E. / Adams, M.W.W. / Kelly, R.M.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tapirin
B: Tapirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0235
Polymers125,8502
Non-polymers1723
Water11,331629
1
A: Tapirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0573
Polymers62,9251
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tapirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9652
Polymers62,9251
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.093, 98.317, 196.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tapirin


Mass: 62925.223 Da / Num. of mol.: 2 / Fragment: C-terminal domain residues 59-634
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor kristjanssonii (strain ATCC 700853 / DSM 12137 / I77R1B) (bacteria)
Strain: ATCC 700853 / DSM 12137 / I77R1B / Gene: Calkr_0826 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: E4S4B2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid pH 3.0 to 4.0 and 10% to 15% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 21, 2017 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→55 Å / Num. obs: 38585 / % possible obs: 100 % / Redundancy: 5.23 % / Rsym value: 0.2419 / Net I/σ(I): 4.89
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 4.26 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 3969 / Rsym value: 0.6461 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WA0

4wa0


Resolution: 2.65→54.425 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.2508 1899 4.94 %
Rwork0.1827 --
obs0.186 38468 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→54.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 8 629 6024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085531
X-RAY DIFFRACTIONf_angle_d0.9867524
X-RAY DIFFRACTIONf_dihedral_angle_d7.7594496
X-RAY DIFFRACTIONf_chiral_restr0.06852
X-RAY DIFFRACTIONf_plane_restr0.007983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71630.37241270.28522545X-RAY DIFFRACTION100
2.7163-2.78970.32691230.26472601X-RAY DIFFRACTION100
2.7897-2.87180.30211320.22832580X-RAY DIFFRACTION100
2.8718-2.96450.29751580.21592569X-RAY DIFFRACTION100
2.9645-3.07050.33521350.22262574X-RAY DIFFRACTION100
3.0705-3.19340.3011370.21852598X-RAY DIFFRACTION100
3.1934-3.33870.27471440.21192554X-RAY DIFFRACTION100
3.3387-3.51470.26781410.17892604X-RAY DIFFRACTION100
3.5147-3.73490.23751370.17142582X-RAY DIFFRACTION100
3.7349-4.02310.21561230.1482615X-RAY DIFFRACTION100
4.0231-4.42780.19361090.13532653X-RAY DIFFRACTION100
4.4278-5.06820.16281430.11182613X-RAY DIFFRACTION99
5.0682-6.38380.2371660.15872655X-RAY DIFFRACTION100
6.3838-54.43620.23081240.21362826X-RAY DIFFRACTION100

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