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- PDB-1oni: Crystal structure of a human p14.5, a translational inhibitor rev... -

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Basic information

Entry
Database: PDB / ID: 1oni
TitleCrystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family
Components14.5 kDa translational inhibitor protein
KeywordsTRANSLATION / YjgF/YER057c/UK114 family / Trichloroacetic acid soluble protein / Translational inhibitor
Function / homology
Function and homology information


Threonine catabolism / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase / L-threonine catabolic process to glycine / organonitrogen compound catabolic process / deaminase activity / response to salt / G1 to G0 transition / response to lipid / long-chain fatty acid binding ...Threonine catabolism / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate/2-iminopropanoate deaminase / L-threonine catabolic process to glycine / organonitrogen compound catabolic process / deaminase activity / response to salt / G1 to G0 transition / response to lipid / long-chain fatty acid binding / mRNA destabilization / mRNA catabolic process / transition metal ion binding / kidney development / lung development / brain development / peroxisome / negative regulation of epithelial cell proliferation / RNA endonuclease activity, producing 3'-phosphomonoesters / negative regulation of translation / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / 2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsManjasetty, B.A. / Delbrueck, H. / Mueller, U. / Erdmann, M.F. / Heinemann, U.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of Homo sapiens protein hp14.5.
Authors: Manjasetty, B.A. / Delbruck, H. / Pham, D.T. / Mueller, U. / Fieber-Erdmann, M. / Scheich, C. / Sievert, V. / Bussow, K. / Niesen, F.H. / Weihofen, W. / Loll, B. / Saenger, W. / Heinemann, U. / Neisen, F.H.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _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: 14.5 kDa translational inhibitor protein
B: 14.5 kDa translational inhibitor protein
C: 14.5 kDa translational inhibitor protein
D: 14.5 kDa translational inhibitor protein
E: 14.5 kDa translational inhibitor protein
F: 14.5 kDa translational inhibitor protein
G: 14.5 kDa translational inhibitor protein
H: 14.5 kDa translational inhibitor protein
I: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,26422
Polymers130,6769
Non-polymers1,58813
Water7,981443
1
A: 14.5 kDa translational inhibitor protein
B: 14.5 kDa translational inhibitor protein
C: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1698
Polymers43,5593
Non-polymers6115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-15 kcal/mol
Surface area15690 Å2
MethodPISA
2
D: 14.5 kDa translational inhibitor protein
E: 14.5 kDa translational inhibitor protein
F: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0477
Polymers43,5593
Non-polymers4884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-14 kcal/mol
Surface area14950 Å2
MethodPISA
3
G: 14.5 kDa translational inhibitor protein
H: 14.5 kDa translational inhibitor protein
I: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0477
Polymers43,5593
Non-polymers4884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-14 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.158, 154.158, 104.559
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
14.5 kDa translational inhibitor protein / p14.5 / UK114 antigen homolog


Mass: 14519.549 Da / Num. of mol.: 9 / Fragment: Translational inhibitor
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN STRUCTURE FACTORY CLONE ID 104124 / Gene: PSP / Plasmid: PSFEP758H0822 / Cellular location (production host): cytoplasm / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1 / References: UniProt: P52758
#2: Chemical
ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.67 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium malonate, sodium benzoate, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.8 mg/mlprotein1drop
22 Msodium malonate1reservoir
30.3 Msodium benzoate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98004
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2002 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 110385 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 22.9
Reflection shellResolution: 1.9→1.92 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.55 / % possible all: 94.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 754078
Reflection shell
*PLUS
% possible obs: 94.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.239 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REFINEMENT WITH TLS PARAMETERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5511 5 %RANDOM
Rwork0.185 ---
all-110333 --
obs-104822 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0.62 Å20 Å2
2---1.24 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8981 0 117 443 9541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229224
X-RAY DIFFRACTIONr_bond_other_d0.0020.028589
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.97712493
X-RAY DIFFRACTIONr_angle_other_deg1.467319982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.09731201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46151627
X-RAY DIFFRACTIONr_chiral_restr0.0940.21472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210316
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021683
X-RAY DIFFRACTIONr_nbd_refined0.2980.31880
X-RAY DIFFRACTIONr_nbd_other0.2180.38235
X-RAY DIFFRACTIONr_nbtor_other0.3160.57
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.5702
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1210.514
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.327
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.59
X-RAY DIFFRACTIONr_mcbond_it0.9151.56022
X-RAY DIFFRACTIONr_mcangle_it1.62729677
X-RAY DIFFRACTIONr_scbond_it2.2433189
X-RAY DIFFRACTIONr_scangle_it3.6924.52829
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 369
Rwork0.242 7101
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)
11.25830.12450.30791.32510.44441.2979-0.00020.06710.0421-0.1365-0.0394-0.0872-0.13960.06110.03960.2355-0.0149-0.02370.17750.05960.083835.12829.95715.401
21.5152-0.25430.55461.66550.05851.4506-0.0926-0.1645-0.08330.26020.02290.06610.0181-0.09450.06960.2626-0.00360.00140.1920.05530.073427.84217.42633.741
31.67660.2980.53941.60950.44141.2539-0.0305-0.011-0.1795-0.0645-0.0068-0.20590.13690.1550.03730.25440.01860.00940.19770.06350.144341.5257.64417.552
41.20030.7033-0.16552.1195-1.07752.3256-0.05260.07010.1632-0.11590.16280.3188-0.0427-0.0211-0.11020.256-0.0124-0.02630.17920.03040.046456.22452.23228.026
51.7906-0.1550.78751.8062-0.33111.84290.21030.1036-0.1834-0.14770.02980.08140.3070.1508-0.24010.30430.0302-0.05680.1977-0.01040.023462.64831.41136.066
61.24660.07360.74162.082-1.24183.0711-0.0010.11280.13080.359-0.1625-0.2258-0.32340.53390.16360.3228-0.0683-0.03290.27890.0150.003672.3150.73144.726
72.72740.2291-0.37971.4850.01741.425-0.12620.0478-0.28190.0292-0.10070.17120.0593-0.16680.2270.2398-0.02330.01470.3039-0.07220.1189-4.9229.86730.044
82.83350.842-0.29812.1937-0.4451.76710.25630.07790.28820.2286-0.07180.4828-0.2914-0.1033-0.18450.34720.0270.07530.2854-0.07850.2177-12.94151.39633.263
91.7339-0.1027-0.3522.59490.38682.41170.14460.26880.1224-0.3317-0.1789-0.0256-0.2667-0.1480.03440.31510.0529-0.01140.34320.00510.07332.69347.37516.631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 12526 - 126
2X-RAY DIFFRACTION2BB25 - 12526 - 126
3X-RAY DIFFRACTION3CC25 - 12526 - 126
4X-RAY DIFFRACTION4DD25 - 12526 - 126
5X-RAY DIFFRACTION5EE25 - 12526 - 126
6X-RAY DIFFRACTION6FF25 - 12526 - 126
7X-RAY DIFFRACTION7GG25 - 12526 - 126
8X-RAY DIFFRACTION8HH25 - 12526 - 126
9X-RAY DIFFRACTION9II25 - 12526 - 126
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.542

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