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- PDB-6xyd: Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific p... -

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Basic information

Entry
Database: PDB / ID: 6xyd
TitleCrystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma cruzi
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Q4D6Q5 / Trypanosoma / neglected diseases
Function / homologymetal ion binding / Paraflagellar rod component
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsRoske, Y. / Heinemann, U. / Andrea, E.D.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)99999.011648/2013-09 Brazil
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma cruzi.
Authors: D'Andrea, E.D. / Roske, Y. / Oliveira, G.A.P. / Cremer, N. / Diehl, A. / Schmieder, P. / Heinemann, U. / Oschkinat, H. / Pires, J.R.
History
DepositionJan 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)53,65810
Polymers53,4804
Non-polymers1786
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.213, 44.771, 68.654
Angle α, β, γ (deg.)90.000, 93.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999264, 0.019172, -0.033226), (0.010357, 0.968816, 0.247566), (0.036936, 0.24704, -0.968301)33.787441, -4.37239, 33.900429
3given(0.000798, 0.106695, -0.994291), (-0.123423, 0.9867, 0.105782), (0.992354, 0.122634, 0.013956)34.031921, 0.27495, 0.48955
4given(-0.017911, -0.132901, 0.990967), (0.126745, 0.982829, 0.1341), (-0.991774, 0.128002, -0.000758)-0.27198, -4.3525, 33.9249

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Components

#1: Protein
Uncharacterized protein


Mass: 13370.087 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Gene: Tc00.1047053511733.90 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4D6Q6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.81→37.07 Å / Num. obs: 36826 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.14 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.085 / Net I/σ(I): 12.9
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.82 / Num. unique obs: 5892 / CC1/2: 0.684 / Rrim(I) all: 0.881 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XYB

6xyb


Resolution: 1.81→37.07 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1842 5 %RANDOM
Rwork0.183 ---
obs0.185 36826 99.6 %-
Displacement parametersBiso max: 138.48 Å2 / Biso mean: 34.18 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.1633 Å20 Å21.1899 Å2
2---0.1418 Å20 Å2
3---1.305 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.81→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 6 313 3690
Biso mean--22.33 42.86 -
Num. residues----421
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1210SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes507HARMONIC5
X-RAY DIFFRACTIONt_it3474HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4127SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3474HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4702HARMONIC30.85
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion15.84
LS refinement shellResolution: 1.81→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.27 152 5.02 %
Rwork0.228 2875 -
all0.23 3027 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.87260.03040.8261.9519-0.30222.410.0809-0.0638-0.05630.1966-0.0708-0.12560.04690.3079-0.0102-0.0261-0.0137-0.0413-0.06730.0002-0.054430.7591-2.719124.4355
21.75950.18391.03911.58770.87582.69730.0091-0.03970.0441-0.0323-0.0650.22880.0341-0.44890.0559-0.06480.0197-0.0267-0.0502-0.012-0.02432.8149-0.87269.4812
32.2625-0.011-1.32661.19830.31353.54090.0160.29510.1418-0.122-0.0303-0.0382-0.0147-0.03110.0143-0.05360.0069-0.0225-0.07250.0226-0.05424.2786-0.68163.465
42.69380.2916-0.22212.67260.03553.00270.0026-0.4798-0.05210.2425-0.05190.23280.3378-0.29460.0493-0.0424-0.02340.0142-0.0482-0.0203-0.11139.0024-3.654730.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 115
2X-RAY DIFFRACTION2{ B|* }B-1 - 115
3X-RAY DIFFRACTION3{ C|* }C-2 - 115
4X-RAY DIFFRACTION4{ D|* }D2 - 116

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