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- PDB-4wa0: The structure of a possible adhesin C-terminal domain from Caldic... -

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Basic information

Entry
Database: PDB / ID: 4wa0
TitleThe structure of a possible adhesin C-terminal domain from Caldicellulosiruptor kronotskyensis
Componentspossible adhesin
KeywordsCELL ADHESION / Beta-helix / Caldicellulosiruptor
Function / homologyAutotransporter, pectate lyase C-like domain superfamily / membrane / metal ion binding / Type 4 fimbrial biogenesis protein PilX N-terminal domain-containing protein
Function and homology information
Biological speciesCaldicellulosiruptor kronotskyensis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Discrete and Structurally Unique Proteins (Tapirins) Mediate Attachment of Extremely Thermophilic Caldicellulosiruptor Species to Cellulose.
Authors: Blumer-Schuette, S.E. / Alahuhta, M. / Conway, J.M. / Lee, L.L. / Zurawski, J.V. / Giannone, R.J. / Hettich, R.L. / Lunin, V.V. / Himmel, M.E. / Kelly, R.M.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.pdbx_ordinal
Revision 1.4Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: possible adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4002
Polymers38,3761
Non-polymers241
Water9,890549
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.507, 75.290, 77.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsStructure contains the C-terminal domain of the protein. Oligomeric state of the full protein is unknown.

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Components

#1: Protein possible adhesin


Mass: 38375.898 Da / Num. of mol.: 1 / Fragment: unp residues 260-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor kronotskyensis (bacteria)
Strain: DSM 18902 / VKM B-2412 / 2002 / Gene: Calkro_0844 / Production host: Escherichia coli (E. coli) / References: UniProt: E4SDB5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS MOLECULE WAS PRODUCED WITH THERMOLYSIN CLEAVAGE FROM A LARGER PROTEIN. THE EXACT SEQUENCE OF ...THIS MOLECULE WAS PRODUCED WITH THERMOLYSIN CLEAVAGE FROM A LARGER PROTEIN. THE EXACT SEQUENCE OF THE CRYSTALLIZED ENTITY IS UNKNOWN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: PEG ion HT screen from Hampton Research (Aliso Viejo, CA) condition G12 containing 0.07 M Citric acid, 0.03 M BIS-TRIS propane, and 16% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 24, 2014
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→55 Å / Num. obs: 40244 / % possible obs: 99.8 % / Redundancy: 8.24 % / Biso Wilson estimate: 14.323 Å2 / Net I/σ(I): 17.48
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.69 % / Mean I/σ(I) obs: 2.36 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PROTEUM PLUS3013.8-1data scaling
Cootmodel building
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→53.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.281 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 1968 4.9 %RANDOM
Rwork0.15 ---
obs0.1522 38105 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.7→53.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 1 549 3228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192972
X-RAY DIFFRACTIONr_bond_other_d0.0020.022794
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9784080
X-RAY DIFFRACTIONr_angle_other_deg0.92836474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24625.738122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6551514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213570
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
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_it1.9891.7621571
X-RAY DIFFRACTIONr_mcbond_other1.9831.7581570
X-RAY DIFFRACTIONr_mcangle_it2.8812.6242004
X-RAY DIFFRACTIONr_mcangle_other2.8832.6292005
X-RAY DIFFRACTIONr_scbond_it2.862.0231401
X-RAY DIFFRACTIONr_scbond_other2.862.0261402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2442.9482077
X-RAY DIFFRACTIONr_long_range_B_refined7.08116.6343665
X-RAY DIFFRACTIONr_long_range_B_other6.60815.223330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 137 -
Rwork0.257 2697 -
obs--96.76 %

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