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- PDB-9n80: Crystal structure of human HRSP12 -

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Basic information

Entry
Database: PDB / ID: 9n80
TitleCrystal structure of human HRSP12
Components2-iminobutanoate/2-iminopropanoate deaminase
KeywordsRNA BINDING PROTEIN / Deaminase / hydrolase
Function / homology
Function and homology information


Threonine catabolism / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / L-threonine catabolic process to glycine / deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome ...Threonine catabolism / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / L-threonine catabolic process to glycine / deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / negative regulation of translation / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / extracellular exosome / 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 superfamily
Similarity search - Domain/homology
2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsSuma, K. / Mugridge, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM143000 United States
CitationJournal: To Be Published
Title: Crystal structure of human HRSP12
Authors: Suma, K. / Jeffrey, S.M.
History
DepositionFeb 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-iminobutanoate/2-iminopropanoate deaminase
B: 2-iminobutanoate/2-iminopropanoate deaminase


Theoretical massNumber of molelcules
Total (without water)32,8892
Polymers32,8892
Non-polymers00
Water3,873215
1
A: 2-iminobutanoate/2-iminopropanoate deaminase

A: 2-iminobutanoate/2-iminopropanoate deaminase

A: 2-iminobutanoate/2-iminopropanoate deaminase


Theoretical massNumber of molelcules
Total (without water)49,3343
Polymers49,3343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7520 Å2
ΔGint-37 kcal/mol
Surface area15230 Å2
MethodPISA
2
B: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase


Theoretical massNumber of molelcules
Total (without water)49,3343
Polymers49,3343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area7850 Å2
ΔGint-28 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.486, 88.486, 88.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

21A-295-

HOH

31A-303-

HOH

41B-239-

HOH

51B-297-

HOH

61B-305-

HOH

71B-306-

HOH

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Components

#1: Protein 2-iminobutanoate/2-iminopropanoate deaminase / 14.5 kDa translational inhibitor protein / hp14.5 / p14.5 / Heat-responsive protein 12 / Reactive ...14.5 kDa translational inhibitor protein / hp14.5 / p14.5 / Heat-responsive protein 12 / Reactive intermediate imine deaminase A homolog / Translation inhibitor L-PSP ribonuclease / UK114 antigen homolog


Mass: 16444.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: his-tagged protein with TEV cleavage site / Source: (gene. exp.) Homo sapiens (human) / Gene: RIDA, HRSP12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P52758, 2-iminobutanoate/2-iminopropanoate deaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.76 Å3/Da / Density % sol: 29.93 % / Description: octahedral blocks
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2 M sodium thiocyanate pH 6.9, 18 % PEG 3350, 30 mM N1-methyladenosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.39→29.5 Å / Num. obs: 46625 / % possible obs: 99.98 % / Redundancy: 37.9 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04376 / Net I/σ(I): 56.71
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 29.5 % / Rmerge(I) obs: 0.6199 / Mean I/σ(I) obs: 5.88 / Num. unique obs: 4619 / CC1/2: 0.953 / CC star: 0.988 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSJun 30, 2024; Fast_DP version 1.6.2data reduction
PHASER2.8.3phasing
XDSJun 30, 2024; Fast_DP version 1.6.2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→29.5 Å / SU ML: 0.1278 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 20.5586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 2019 4.29 %
Rwork0.1911 45057 -
obs0.1923 46625 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.04 Å2
Refinement stepCycle: LAST / Resolution: 1.39→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 0 215 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482067
X-RAY DIFFRACTIONf_angle_d0.7712803
X-RAY DIFFRACTIONf_chiral_restr0.0697331
X-RAY DIFFRACTIONf_plane_restr0.0048364
X-RAY DIFFRACTIONf_dihedral_angle_d5.5572295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.2441410.21563156X-RAY DIFFRACTION99.43
1.42-1.460.25021430.21463182X-RAY DIFFRACTION100
1.46-1.50.24021450.20383190X-RAY DIFFRACTION100
1.5-1.550.2511410.20583187X-RAY DIFFRACTION100
1.55-1.60.22741420.19663228X-RAY DIFFRACTION100
1.61-1.670.23291440.2043178X-RAY DIFFRACTION100
1.67-1.740.26591430.21613181X-RAY DIFFRACTION100
1.75-1.840.25221440.21633225X-RAY DIFFRACTION100
1.84-1.950.21011410.19523190X-RAY DIFFRACTION100
1.95-2.10.21291390.18923226X-RAY DIFFRACTION100
2.1-2.310.18951470.18393234X-RAY DIFFRACTION100
2.31-2.650.22741480.19973237X-RAY DIFFRACTION100
2.65-3.330.25751500.19543262X-RAY DIFFRACTION100
3.34-29.50.17681510.17063381X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.7393668461 Å / Origin y: 8.27864333302 Å / Origin z: -15.7656583139 Å
111213212223313233
T0.126449173146 Å2-0.0031695437037 Å20.00108053257129 Å2-0.103031630816 Å2-0.00366308775415 Å2--0.108611684962 Å2
L0.148315503411 °2-0.20625513717 °2-0.0216347534866 °2-0.392111117274 °20.046351343026 °2---0.0390547712055 °2
S0.0282687608473 Å °-0.000782216906947 Å °-0.00294369647423 Å °-0.0251503710992 Å °-0.00424553767606 Å °0.0178693956903 Å °-0.0178712563531 Å °-0.0117699442571 Å °0.0260376914571 Å °
Refinement TLS groupSelection details: all

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