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- PDB-5vf4: Thermus aquaticus variable protein (TaqVP) from diversity-generat... -

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Basic information

Entry
Database: PDB / ID: 5vf4
TitleThermus aquaticus variable protein (TaqVP) from diversity-generating retroelements (DGR)
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / CLec-fold / Thermostable / DNA diversification
Function / homologySulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / ACETATE ION / FGE-sulfatase domain-containing protein
Function and homology information
Biological speciesThermus aquaticus Y51MC23 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsHanda, S. / Ghosh, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI096838 United States
CitationJournal: PLoS ONE / Year: 2019
Title: Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein.
Authors: Handa, S. / Shaw, K.L. / Ghosh, P.
History
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,00442
Polymers163,9124
Non-polymers2,09238
Water2,954164
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3538
Polymers40,9781
Non-polymers3757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,58912
Polymers40,9781
Non-polymers61211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98419
Polymers40,9781
Non-polymers1,00618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0773
Polymers40,9781
Non-polymers992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.039, 155.039, 202.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Uncharacterized protein


Mass: 40977.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus Y51MC23 (bacteria) / Gene: TaqDRAFT_4799, TaqDRAFT_5434 / Production host: Escherichia coli (E. coli) / References: UniProt: B7A5T1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 4.32 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) 2-methyl-2,4-pentanediol, 20 mm CaCl2, 100 mM Sodium Acetate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.81→134.27 Å / Num. obs: 132418 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.98 / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→80.814 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 3829 2.89 %
Rwork0.1778 --
obs0.1793 128585 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→80.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11381 0 128 164 11673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911757
X-RAY DIFFRACTIONf_angle_d1.22416014
X-RAY DIFFRACTIONf_dihedral_angle_d13.0724130
X-RAY DIFFRACTIONf_chiral_restr0.0511733
X-RAY DIFFRACTIONf_plane_restr0.0062128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.81-2.91040.3743800.31491279412794
2.9104-3.0270.32783690.286612910
3.027-3.16470.31253860.258512900
3.1647-3.33160.26933840.23512784
3.3316-3.54030.27723950.207312921
3.5403-3.81370.22143910.172412834
3.8137-4.19750.2063780.144212897
4.1975-4.80480.16513800.122712843
4.8048-6.05320.17983970.130312798
6.0532-80.84740.2063690.158312893
Refinement TLS params.Method: refined / Origin x: 55.5268 Å / Origin y: 74.5398 Å / Origin z: 74.1778 Å
111213212223313233
T0.221 Å20.1117 Å2-0.0358 Å2-0.1913 Å20.03 Å2--0.1848 Å2
L0.1834 °20.0271 °20.0453 °2-0.133 °20.0805 °2--0.2578 °2
S-0.0038 Å °0.0435 Å °0.0045 Å °-0.1562 Å °-0.0589 Å °0.0038 Å °-0.1481 Å °0.1487 Å °-0.0014 Å °
Refinement TLS groupSelection details: all

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