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- PDB-1yzv: HYPOTHETICAL PROTEIN FROM TRYPANOSOMA CRUZI -

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Basic information

Entry
Database: PDB / ID: 1yzv
TitleHYPOTHETICAL PROTEIN FROM TRYPANOSOMA CRUZI
ComponentsHYPOTHETICAL PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homologyIsochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Ribonuclease mar1, putative
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsCaruthers, J. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily.
Authors: Caruthers, J. / Zucker, F. / Worthey, E. / Myler, P.J. / Buckner, F. / Van Voorhuis, W. / Mehlin, C. / Boni, E. / Feist, T. / Luft, J. / Gulde, S. / Lauricella, A. / Kaluzhniy, O. / ...Authors: Caruthers, J. / Zucker, F. / Worthey, E. / Myler, P.J. / Buckner, F. / Van Voorhuis, W. / Mehlin, C. / Boni, E. / Feist, T. / Luft, J. / Gulde, S. / Lauricella, A. / Kaluzhniy, O. / Anderson, L. / Le Trong, I. / Holmes, M.A. / Earnest, T. / Soltis, M. / Hodgson, K.O. / Hol, W.G. / Merritt, E.A.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of this protein can be found at GeneDB with sequence ID Tc00.1047053505945.20.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6572
Polymers22,5611
Non-polymers961
Water2,990166
1
A: HYPOTHETICAL PROTEIN
hetero molecules

A: HYPOTHETICAL PROTEIN
hetero molecules

A: HYPOTHETICAL PROTEIN
hetero molecules

A: HYPOTHETICAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6308
Polymers90,2454
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
Buried area8070 Å2
ΔGint-103 kcal/mol
Surface area28550 Å2
MethodPISA
2
A: HYPOTHETICAL PROTEIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)543,77848
Polymers541,47224
Non-polymers2,30624
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area67750 Å2
ΔGint-724 kcal/mol
Surface area152000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.142, 121.142, 121.142
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number207
Space group name H-MP432
DetailsThe biological assembly is a tetramer generated by the crystallographic 4-fold

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Components

#1: Protein HYPOTHETICAL PROTEIN


Mass: 22561.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D3U8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 ul protein 19 mg/ml 0.4 ul crystallization buffer 20% PEG 4000, 100 mM CaCl2, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→18.47 Å / Num. obs: 21028 / % possible obs: 99 % / Redundancy: 9.9 % / Biso Wilson estimate: 18.02 Å2 / Rmerge(I) obs: 0.183 / Net I/σ(I): 12

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
MOSFLMdata reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→18.47 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.175 / WRfactor Rwork: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.113 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1868 1056 5.029 %
Rwork0.1568 --
obs-20998 99.413 %
Solvent computationSolvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 25.918 Å2
Refinement stepCycle: LAST / Resolution: 2.001→18.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 5 166 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221531
X-RAY DIFFRACTIONr_bond_other_d0.0010.021409
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9612075
X-RAY DIFFRACTIONr_angle_other_deg0.91333286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13224.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03815265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.867156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021678
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02294
X-RAY DIFFRACTIONr_nbd_refined0.2170.2311
X-RAY DIFFRACTIONr_nbd_other0.1750.21390
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2758
X-RAY DIFFRACTIONr_nbtor_other0.0850.2869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.217
X-RAY DIFFRACTIONr_mcbond_it2.6351.51249
X-RAY DIFFRACTIONr_mcbond_other0.7031.5395
X-RAY DIFFRACTIONr_mcangle_it2.97621571
X-RAY DIFFRACTIONr_mcangle_other1.3321333
X-RAY DIFFRACTIONr_scbond_it5.3323643
X-RAY DIFFRACTIONr_scbond_other1.79931210
X-RAY DIFFRACTIONr_scangle_it6.7994.5504
X-RAY DIFFRACTIONr_scangle_other3.344.51953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.001-2.1070.2281520.1822768298397.888
2.107-2.2330.2111380.1612665281799.503
2.233-2.3850.2061500.1552517267999.552
2.385-2.5730.1961410.1522345249299.759
2.573-2.8130.2091040.1552199231399.568
2.813-3.1360.183920.1552021212099.67
3.136-3.6030.152870.1511792188499.735
3.603-4.3720.173860.1391561164899.939
4.372-6.0170.177580.1611255131499.924
6.017-18.4740.166480.18881987299.427
Refinement TLS params.Method: refined / Origin x: 72.3792 Å / Origin y: 41.4615 Å / Origin z: 102.7344 Å
111213212223313233
T-0.0157 Å20.0041 Å20.0019 Å2--0.0065 Å2-0.0048 Å2---0.0273 Å2
L0.6055 °20.2534 °20.0215 °2-0.3263 °2-0.0558 °2--0.2379 °2
S-0.0051 Å °0.0131 Å °-0.0653 Å °-0.006 Å °0.0167 Å °-0.0378 Å °-0.0016 Å °0.0139 Å °-0.0116 Å °
Refinement TLS groupSelection: ALL

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