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- PDB-1qah: CRYSTAL STRUCTURE OF PERCHLORIC ACID SOLUBLE PROTEIN-A TRANSLATIO... -

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Basic information

Entry
Database: PDB / ID: 1qah
TitleCRYSTAL STRUCTURE OF PERCHLORIC ACID SOLUBLE PROTEIN-A TRANSLATIONAL INHIBITOR
ComponentsPERCHLORIC ACID SOLUBLE PROTEIN
KeywordsALPHA-BETA STRUCTURE
Function / homology
Function and homology information


Threonine catabolism / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / cation binding / deaminase activity / response to salt / G1 to G0 transition / long-chain fatty acid binding / response to lipid ...Threonine catabolism / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / cation binding / deaminase activity / response to salt / G1 to G0 transition / long-chain fatty acid binding / response to lipid / mRNA destabilization / mRNA catabolic process / transition metal ion binding / lung development / kidney development / lipid metabolic process / negative regulation of epithelial cell proliferation / peroxisome / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / negative regulation of translation / mitochondrial matrix / mRNA binding / mitochondrion / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsDjinovic Carugo, K. / Oka, T.
CitationJournal: To be Published
Title: Crystal Structure of Perchloric Acid Soluble Protein-a Translational Inhibitor
Authors: Djinovic Carugo, K. / Oka, T.
History
DepositionMar 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 28, 2021Group: Refinement description / Category: refine
Item: _refine.details / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PERCHLORIC ACID SOLUBLE PROTEIN
B: PERCHLORIC ACID SOLUBLE PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,3682
Polymers28,3682
Non-polymers00
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PERCHLORIC ACID SOLUBLE PROTEIN

B: PERCHLORIC ACID SOLUBLE PROTEIN

B: PERCHLORIC ACID SOLUBLE PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,5533
Polymers42,5533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area6680 Å2
ΔGint-38 kcal/mol
Surface area14680 Å2
MethodPISA, PQS
3
A: PERCHLORIC ACID SOLUBLE PROTEIN

A: PERCHLORIC ACID SOLUBLE PROTEIN

A: PERCHLORIC ACID SOLUBLE PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,5533
Polymers42,5533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area6600 Å2
ΔGint-28 kcal/mol
Surface area15080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.743, 89.743, 89.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-323-

HOH

31A-324-

HOH

41A-325-

HOH

51A-327-

HOH

61B-311-

HOH

71B-312-

HOH

81B-313-

HOH

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Components

#1: Protein PERCHLORIC ACID SOLUBLE PROTEIN


Mass: 14184.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER, KIDNEY / References: UniProt: P52759
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: VAPOR DIFFUSION, HANGING DROP, PH 4.5, 293K, PEG 8000, SODIUM ACETATE, AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9183
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 1.8→63.2 Å / Num. all: 22619 / Num. obs: 22619 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.34 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 34.14
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.93 % / Rmerge(I) obs: 0.277 / % possible all: 96.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
WARPmodel building
REFMACrefinement
ARP/wARPmodel building
RefinementResolution: 1.8→40 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27614 1134 -RANDOM
Rwork0.19054 ---
all-22116 --
obs-22116 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 0 379 2325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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