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- PDB-2je0: Crystal Structure of pp32 -

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Basic information

Entry
Database: PDB / ID: 2je0
TitleCrystal Structure of pp32
ComponentsACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
KeywordsNUCLEAR PROTEIN
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / nucleocytoplasmic transport / regulation of apoptotic process / histone binding / intracellular signal transduction / perinuclear region of cytoplasm / endoplasmic reticulum / RNA binding / nucleoplasm / nucleus / 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: 2.4 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: Refinement description / 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
E: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
F: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,89517
Polymers101,8826
Non-polymers1,01311
Water5,531307
1
A: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1653
Polymers16,9801
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
MethodPISA
3
C: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1653
Polymers16,9801
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2574
Polymers16,9801
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 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
MethodPISA
6
F: ACIDIC LEUCINE-RICH NUCLEAR PHOSPHOPROTEIN 32 FAMILY MEMBER A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1653
Polymers16,9801
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.501, 183.237, 67.477
Angle α, β, γ (deg.)90.00, 104.39, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

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: 3 / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper: (Code: given
Matrix: (-0.51187, -0.85906, 0.0008), (-0.85899, 0.51184, 0.01285), (-0.01145, 0.00589, -0.99992)
Vector: 13.38251, 7.36462, 65.30293)

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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.: 6 / 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.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.03 Å3/Da / Density % sol: 59.14 %
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: 2.4→25 Å / Num. obs: 48207 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 93.7

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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: 2.4→25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 26.537 / SU ML: 0.286 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2426 5 %RANDOM
Rwork0.218 ---
obs0.221 45760 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å21.42 Å2
2---2.19 Å20 Å2
3---4.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 66 307 7507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.0219769
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66325.965342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.487151458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5561542
X-RAY DIFFRACTIONr_chiral_restr0.1020.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22999
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24810
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3681.54598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65527188
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47832920
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3984.52581
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
5E596tight positional0.040.05
6F596tight positional0.030.05
1A593loose positional0.515
2B593loose positional0.545
3C593loose positional0.565
4D593loose positional0.675
5E593loose positional0.585
6F593loose positional0.525
1A596tight thermal0.060.5
2B596tight thermal0.060.5
3C596tight thermal0.050.5
4D596tight thermal0.060.5
5E596tight thermal0.050.5
6F596tight thermal0.050.5
1A593loose thermal1.0610
2B593loose thermal1.210
3C593loose thermal1.0610
4D593loose thermal1.0910
5E593loose thermal0.9610
6F593loose thermal0.9710
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 150 -
Rwork0.315 3068 -
obs--89.12 %
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)
14.81292.80481.1195.34831.07031.6718-0.01560.01910.26660.0087-0.09160.0582-0.121-0.24830.1072-0.14810.02640.0039-0.1494-0.0277-0.254121.997-0.37716.515
28.04260.23281.31472.08080.49812.1592-0.05090.07160.1477-0.028-0.0277-0.0188-0.30630.07250.0786-0.1147-0.0051-0.0216-0.18380.02-0.32022.454-11.52348.504
34.1707-3.017-0.565110.24022.01331.5379-0.01360.1784-0.0374-0.0791-0.19320.48650.1845-0.2270.2068-0.1441-0.01270.0114-0.123-0.0306-0.1538-20.423-51.02616.464
49.7613-0.0429-1.17592.859-0.2751.43070.0098-0.1156-0.26140.1612-0.10070.01450.293-0.00610.0909-0.1111-0.00390.0256-0.1628-0.029-0.244334.009-21.4948.584
54.5836-2.5450.37648.7182-1.56831.4884-0.11310.12880.2892-0.1721-0.1272-0.486-0.17880.22870.2403-0.0934-0.0049-0.0305-0.11590.0587-0.15263.854-73.48717.079
65.90894.0308-1.39087.7188-1.87361.7402-0.16420.1013-0.591-0.2043-0.0307-0.50540.14210.18220.1948-0.13990.0198-0.0022-0.1680.01-0.126514.555-32.63716.612
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
5X-RAY DIFFRACTION5E1 - 149
6X-RAY DIFFRACTION6F1 - 149

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