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- PDB-2g80: Crystal structure of UTR4 protein (Unknown transcript 4 protein) ... -

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Basic information

Entry
Database: PDB / ID: 2g80
TitleCrystal structure of UTR4 protein (Unknown transcript 4 protein) (yel038w) from Saccharomyces cerevisiae at 2.28 A resolution
ComponentsProtein UTR4
KeywordsHYDROLASE / yel038w / UTR4 protein (Unknown transcript 4 protein) / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


Methionine salvage pathway / acireductone synthase / acireductone synthase activity / 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity / 2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / magnesium ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #60 / Enolase-phosphatase E1 / Enolase-phosphatase E1, eukaryotes / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #60 / Enolase-phosphatase E1 / Enolase-phosphatase E1, eukaryotes / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enolase-phosphatase E1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of UTR4 protein (Unknown transcript 4 protein) (yel038w) from Saccharomyces cerevisiae at 2.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein UTR4
B: Protein UTR4
C: Protein UTR4
D: Protein UTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,58913
Polymers112,9044
Non-polymers6849
Water5,765320
1
A: Protein UTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6053
Polymers28,2261
Non-polymers3792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein UTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2502
Polymers28,2261
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein UTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3674
Polymers28,2261
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein UTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3674
Polymers28,2261
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.688, 102.016, 77.227
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 19 - 240 / Label seq-ID: 31 - 252

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Protein UTR4 / Unknown transcript 4 protein


Mass: 28226.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UTR4 / Production host: Escherichia coli (E. coli) / References: UniProt: P32626
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 21.00% PEG 3350, 0.10M NP_Magnesium Nitrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→61.54 Å / Num. obs: 52775 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
2.28-2.43.20.3591.72446276730.35999.9
2.4-2.553.70.2512.52662272670.251100
2.55-2.733.70.2381.82494868300.238100
2.73-2.943.70.1255.22341863600.125100
2.94-3.223.70.0926.72157358760.09299.9
3.22-3.63.70.0934.11934452800.09399.9
3.6-4.163.60.0914.61711847070.09199.9
4.16-5.13.70.05610.71450839720.05699.9
5.1-7.213.60.05510.41111530830.05599.9
7.21-102.063.40.04612.8584917270.04699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1zs9A

Resolution: 2.28→61.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.84 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUES 1-15 IN CHAIN A, 1-17 IN CHAIN B AND C, AND 1-17 AND 227-229 IN CHAIN D ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 3. A ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUES 1-15 IN CHAIN A, 1-17 IN CHAIN B AND C, AND 1-17 AND 227-229 IN CHAIN D ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 3. A MG ION FROM THE CRYSTALLIZATION SOLUTION IS OCTAHEDERALLY COORDINATED TO THE SIDECHAINS OF ASP 25 AND ASP 200, THE BACKBONE CARBONYL OXYGEN OF GLU 27, AND THREE WATER MOLECULES. 4. A PEG 3350 MOLECULE FROM THE CRYSTALLIZATION SOLUTION IS LOCATED NEAR VAL 114 IN SUBUNIT A, AND IS PARTIALLY MODELED AS PE4. 5. UNEXPLAINED DIFFERENCE DENSITY IN THE VICINITY OF THE SIDECHAINS OF HIS 79 AND GLU 82 ON THE D SUBUNIT WAS OBSERVED, AND THIS DENSITY WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2673 5.1 %RANDOM
Rwork0.177 ---
obs0.18 52503 99.87 %-
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: 37.416 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å2-1 Å2
2---1.76 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.28→61.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 26 320 7234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227087
X-RAY DIFFRACTIONr_bond_other_d0.0030.026282
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9659635
X-RAY DIFFRACTIONr_angle_other_deg1.196314652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8015895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32125.449312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.746151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6781515
X-RAY DIFFRACTIONr_chiral_restr0.1050.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027954
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021365
X-RAY DIFFRACTIONr_nbd_refined0.1730.21242
X-RAY DIFFRACTIONr_nbd_other0.1220.25725
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23392
X-RAY DIFFRACTIONr_nbtor_other0.0710.23596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2333
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1380.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.217
X-RAY DIFFRACTIONr_mcbond_it1.82634747
X-RAY DIFFRACTIONr_mcbond_other0.42731807
X-RAY DIFFRACTIONr_mcangle_it2.75457199
X-RAY DIFFRACTIONr_scbond_it4.8482864
X-RAY DIFFRACTIONr_scangle_it6.423112433
Refine LS restraints NCS

Ens-ID: 1 / Number: 3136 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.865
2BLOOSE POSITIONAL1.025
3CLOOSE POSITIONAL15
4DLOOSE POSITIONAL0.935
1ALOOSE THERMAL2.7310
2BLOOSE THERMAL3.0810
3CLOOSE THERMAL2.4410
4DLOOSE THERMAL2.5410
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 207 -
Rwork0.213 3703 -
obs-3910 99.82 %
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)
11.35510.08120.24650.998-0.09480.97830.03330.0790.0365-0.0491-0.110.0320.0248-0.05520.0766-0.1844-0.01590.0158-0.0392-0.002-0.162120.25-4.85727.504
21.04260.0606-0.11312.25480.35410.4268-0.0310.0703-0.1767-0.1440.1312-0.02860.00390.0483-0.1003-0.1493-0.0093-0.0299-0.0174-0.0037-0.089746.763-16.45532.854
31.41360.14840.03081.49960.55441.47170.1245-0.1754-0.01950.0755-0.1136-0.03960.21390.0428-0.0109-0.0736-0.043-0.01960.01820.0103-0.17323.827-39.45610.568
41.14190.24590.17881.72050.68741.0559-0.02020.0330.0664-0.29610.0378-0.2567-0.21920.1777-0.0175-0.0146-0.00030.04080.08130.0336-0.076411.524-27.77-15.185
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA17 - 24129 - 253
22BB18 - 24130 - 253
33CC18 - 24130 - 253
44DD18 - 22630 - 238
54DD230 - 241242 - 253

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