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

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Basic information

Entry
Database: PDB / ID: 6xyb
TitleCrystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma cruzi
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Q4D6Q5 / Trypanosoma / neglected diseases
Function / homologymetal ion binding / IODIDE ION / : / Paraflagellar rod component
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsRoske, Y. / Heinemann, U.
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 1.2Nov 6, 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 / 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_entry_details.has_protein_modification / _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

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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)53,85710
Polymers53,4804
Non-polymers3776
Water4,017223
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)66.701, 44.487, 69.544
Angle α, β, γ (deg.)90.000, 93.460, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A7 - 38
2114B7 - 38
3114C7 - 38
4114D7 - 38
1214A53 - 67
2214B53 - 67
3214C53 - 67
4214D53 - 67
1314A72 - 118
2314B72 - 118
3314C72 - 118
4314D72 - 118

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.023277, 0.166414, -0.985781), (-0.115263, 0.979026, 0.167996), (0.993062, 0.117534, -0.003608)-31.92605, 1.11926, -2.42121
3given(0.037601, -0.106897, 0.993559), (0.136457, 0.985498, 0.100866), (-0.989932, 0.131785, 0.051643)2.81193, 3.61132, -30.19047
4given(-0.998824, 0.018568, 0.044792), (0.029487, 0.965924, 0.25714), (-0.038491, 0.258159, -0.965335)-28.29781, 4.67251, -33.838181

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 5000 MME, 0.2 M potassium iodide

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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 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.46→34.71 Å / Num. obs: 70953 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rrim(I) all: 0.067 / Net I/σ(I): 10.8
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 3.5 % / Num. unique obs: 11262 / CC1/2: 0.642 / Rrim(I) all: 0.824 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→34.71 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.374 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 2721 5 %RANDOM
Rwork0.1433 ---
obs0.1454 51685 77.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.39 Å2 / Biso mean: 27.293 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å2-0 Å2-2.7 Å2
2--1.1 Å20 Å2
3---2.14 Å2
Refinement stepCycle: final / Resolution: 1.47→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 6 223 3537
Biso mean--12.89 36.83 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133445
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173161
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.6444685
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5747344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12921.486175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6661524
X-RAY DIFFRACTIONr_chiral_restr0.1030.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023826
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02750
X-RAY DIFFRACTIONr_rigid_bond_restr6.93536603
Refine LS restraints NCS

Ens-ID: 1 / Number: 1265 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.560.5
2BMEDIUM POSITIONAL0.680.5
3CMEDIUM POSITIONAL0.560.5
4DMEDIUM POSITIONAL0.80.5
1AMEDIUM THERMAL7.662
2BMEDIUM THERMAL13.722
3CMEDIUM THERMAL8.162
4DMEDIUM THERMAL82
LS refinement shellResolution: 1.47→1.506 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.311 201 -
Rwork0.197 3814 -
obs--77.95 %
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)
10.09740.03360.09540.09760.02510.11470.0036-0.00770.0019-0.0059-0.00760.00170.0045-0.01550.0040.00780.0008-0.00530.0081-0.00150.0042-28.1979-0.2187-25.3133
20.1235-0.0247-0.01530.02930.02660.036-0.0067-0.0307-0.01190.00610.00210.01010.006-0.01310.00460.01240.0010.00020.02450.00510.0076-22.2292-3.0202-3.6288
30.23030.0016-0.13270.09890.04660.2902-0.0010.0206-0.00060.0027-0.0013-0.0054-0.0028-0.00320.00220.0040.0008-0.00230.00750.00150.0022-6.73650.2541-31.4428
40.06920.01230.03840.04990.01150.02860.00220.0022-0.00290.0073-0-0.00130.00340.0092-0.00220.01030.0001-0.0050.00990.00030.0026-0.0092-2.1472-9.8701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 115
2X-RAY DIFFRACTION2B1 - 115
3X-RAY DIFFRACTION3C-2 - 115
4X-RAY DIFFRACTION4D0 - 114

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