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- PDB-2je1: The crystal Structure of the tumor supressor protein pp32 (Anp32a... -

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Basic information

Entry
Database: PDB / ID: 2je1
TitleThe crystal Structure of the tumor supressor protein pp32 (Anp32a) :structural insights into the Anp32 family of proteins
ComponentsACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
KeywordsNUCLEAR PROTEIN / LEUCINE-RICH REPEAT / LRR / LANP / PHAPI / ANP32 / PHOSPHORYLATION
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / nucleocytoplasmic transport / histone binding / regulation of apoptotic process / intracellular signal transduction / perinuclear region of cytoplasm / endoplasmic reticulum / DNA-templated transcription / RNA binding / nucleoplasm ...HuR (ELAVL1) binds and stabilizes mRNA / nucleocytoplasmic transport / histone binding / regulation of apoptotic process / intracellular signal transduction / perinuclear region of cytoplasm / endoplasmic reticulum / DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Acidic leucine-rich nuclear phosphoprotein 32 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Acidic leucine-rich nuclear phosphoprotein 32 family member A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsHuyton, T. / Wolberger, C.
CitationJournal: Protein Sci. / Year: 2007
Title: The Crystal Structure of the Tumor Suppressor Protein Pp32 (Anp32A): Structural Insights Into Anp32 Family of Proteins.
Authors: Huyton, T. / Wolberger, C.
History
DepositionJan 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
B: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
C: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
D: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0145
Polymers67,9224
Non-polymers921
Water2,612145
1
A: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0722
Polymers16,9801
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A


Theoretical massNumber of molelcules
Total (without water)16,9801
Polymers16,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A


Theoretical massNumber of molelcules
Total (without water)16,9801
Polymers16,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A


Theoretical massNumber of molelcules
Total (without water)16,9801
Polymers16,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.506, 106.506, 133.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 2 / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149

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

NCS oper: (Code: given
Matrix: (-0.99997, -0.00783, 0.00045), (0.00784, -0.99979, 0.01909), (0.0003, 0.01909, 0.99982)
Vector: 53.44123, 30.35955, -0.35606)

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Components

#1: Protein
ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A / POTENT HEAT-STABLE PROTEIN PHOSPHATASE 2A INHIBITOR I1PP2A / ACIDIC NUCLEAR PHOSPHOPROTEIN PP32 / ...POTENT HEAT-STABLE PROTEIN PHOSPHATASE 2A INHIBITOR I1PP2A / ACIDIC NUCLEAR PHOSPHOPROTEIN PP32 / LEUCINE-RICH ACIDIC NUCLEAR PROTEIN / LANP / PUTATIVE HLA-DR-ASSOCIATED PROTEIN I / PHAPI / MAPMODULIN / PP32


Mass: 16980.375 Da / Num. of mol.: 4 / Fragment: LRR DOMAIN, RESIDUES 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P39687
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.17 Å3/Da / Density % sol: 60.94 %
Crystal growpH: 5.5 / Details: pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2006 / Details: BENT CONICAL SI-MIRROR (RH COATED)
RadiationMonochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 23193 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→25 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 2.69→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.881 / SU B: 29.233 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.908 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1189 5.1 %RANDOM
Rwork0.238 ---
obs0.241 21976 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.69→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 6 145 4907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4852.0166405
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75726.621219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.82115932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023455
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22002
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23138
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3531.53065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5724782
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18331852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9364.51623
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A596tight positional0.030.05
2B596tight positional0.030.05
3C596tight positional0.030.05
4D596tight positional0.030.05
1A570medium positional0.380.5
2B570medium positional0.430.5
3C570medium positional0.440.5
4D570medium positional0.440.5
1A596tight thermal0.050.5
2B596tight thermal0.050.5
3C596tight thermal0.050.5
4D596tight thermal0.050.5
1A570medium thermal0.422
2B570medium thermal0.382
3C570medium thermal0.382
4D570medium thermal0.342
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 86
Rwork0.297 1636
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)
18.13481.1805-1.48382.1314-0.32632.6266-0.1146-0.255-0.53820.1064-0.0376-0.14690.4784-0.10180.1522-0.02540.00190.0571-0.12630.015-0.066642.50710.50.838
29.67871.45222.01852.30150.19851.7852-0.3343-0.43790.6866-0.03040.06980.105-0.3647-0.05750.2645-0.0130.04-0.0231-0.0237-0.047-0.073310.87420.1940.712
35.10793.63981.01825.30891.03772.1759-0.1180.08010.4107-0.2296-0.03160.4326-0.1417-0.34240.1496-0.08910.0416-0.0467-0.0448-0.036-0.049730.32931.565-31.2
45.09994.07-1.30256.551-1.83351.9742-0.2243-0.1057-0.3784-0.4581-0.0068-0.47750.23030.29340.23110.00990.0350.0572-0.0456-0.002-0.083722.915-0.679-31.05
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 149
2X-RAY DIFFRACTION2B1 - 149
3X-RAY DIFFRACTION3C1 - 149
4X-RAY DIFFRACTION4D1 - 149

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