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- PDB-2okv: c-Myc DNA Unwinding Element Binding Protein -

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Basic information

Entry
Database: PDB / ID: 2okv
Titlec-Myc DNA Unwinding Element Binding Protein
ComponentsProbable D-tyrosyl-tRNA(Tyr) deacylase 1
KeywordsHYDROLASE / DNA replication / DUE / ATPase / tRNA Deacylase
Function / homology
Function and homology information


D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / aminoacyl-tRNA editing activity / DNA replication / tRNA binding / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
D-aminoacyl-tRNA deacylase DTD / D-Tyr-tRNA(Tyr) deacylase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-aminoacyl-tRNA deacylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsBae, B. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure and Function of the c-myc DNA-unwinding Element-binding Protein DUE-B.
Authors: Kemp, M. / Bae, B. / Yu, J.P. / Ghosh, M. / Leffak, M. / Nair, S.K.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
B: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
C: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
D: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9368
Polymers93,8384
Non-polymers974
Water6,485360
1
A: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
B: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9684
Polymers46,9192
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-12 kcal/mol
Surface area13650 Å2
MethodPISA
2
C: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
D: Probable D-tyrosyl-tRNA(Tyr) deacylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9684
Polymers46,9192
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-10 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.813, 77.813, 106.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsBiological unit is a dimer composed of chains A+B or C+D

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Components

#1: Protein
Probable D-tyrosyl-tRNA(Tyr) deacylase 1 / DNA Unwinding Element Binding Protein


Mass: 23459.596 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARS2, C20orf88 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8TEA8, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 8000, 200 mM KCl, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 135 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 50139 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 40
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 6 / Num. unique all: 5037 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.391 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23675 2446 5.1 %RANDOM
Rwork0.20477 ---
obs0.20641 45864 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.089 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 4 360 5076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224796
X-RAY DIFFRACTIONr_bond_other_d0.0010.023
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9646452
X-RAY DIFFRACTIONr_angle_other_deg0.96936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.64224.661221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46315906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111529
X-RAY DIFFRACTIONr_chiral_restr0.1140.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023
X-RAY DIFFRACTIONr_nbd_refined0.2180.22215
X-RAY DIFFRACTIONr_nbd_other0.1790.26
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23221
X-RAY DIFFRACTIONr_nbtor_other0.2370.23
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2355
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.226
X-RAY DIFFRACTIONr_mcbond_it0.71.53049
X-RAY DIFFRACTIONr_mcbond_other0.0281.53
X-RAY DIFFRACTIONr_mcangle_it1.19424769
X-RAY DIFFRACTIONr_scbond_it1.98331947
X-RAY DIFFRACTIONr_scangle_it3.0574.51683
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 188 -
Rwork0.223 3336 -
obs--99.66 %
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)
11.7927-0.05880.54523.28140.63073.05760.1453-0.2368-0.22060.1142-0.11760.30320.0858-0.5448-0.0277-0.1527-0.0277-0.0304-0.1840.0417-0.1485-13.25526.4497-0.2222
21.71371.15880.36172.40131.065.01450.3111-0.27320.03970.2622-0.154-0.02010.0492-0.1929-0.1571-0.104-0.0757-0.076-0.2330.0311-0.14920.151226.716314.7133
33.0240.5673-0.22562.0503-0.71032.95420.02050.0546-0.3831-0.30780.02180.04780.52260.1969-0.0423-0.1512-0.0226-0.0515-0.18280.0115-0.146429.553646.68928.7316
41.21440.9623-0.75212.9685-0.90485.1054-0.0460.03190.0673-0.45840.1821-0.02260.20740.0684-0.1361-0.1473-0.0926-0.069-0.20450.0478-0.147223.040258.4751-6.0934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1491 - 149
2X-RAY DIFFRACTION2BB1 - 1501 - 150
3X-RAY DIFFRACTION3CC1 - 1491 - 149
4X-RAY DIFFRACTION4DD1 - 1491 - 149

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