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- PDB-2j9q: A novel conformation for the TPR domain of pex5p -

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Basic information

Entry
Database: PDB / ID: 2j9q
TitleA novel conformation for the TPR domain of pex5p
ComponentsPEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
KeywordsPROTEIN TRANSPORT / TRANSPORT / ZELLWEGER SYNDROME
Function / homology
Function and homology information


protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome matrix targeting signal-1 binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix, docking / protein import into peroxisome matrix ...protein import into peroxisome matrix, substrate release / protein import into peroxisome matrix, translocation / peroxisome matrix targeting signal-1 binding / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / peroxisome targeting sequence binding / protein targeting to peroxisome / protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix, docking / protein import into peroxisome matrix / protein carrier chaperone / very long-chain fatty acid metabolic process / cerebral cortex neuron differentiation / cell development / pexophagy / positive regulation of multicellular organism growth / mitochondrial membrane organization / endoplasmic reticulum organization / peroxisomal membrane / neuromuscular process / fatty acid beta-oxidation / cerebral cortex cell migration / peroxisomal matrix / negative regulation of protein-containing complex assembly / Pexophagy / Peroxisomal protein import / protein tetramerization / neuron migration / small GTPase binding / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / Golgi apparatus / enzyme binding / protein-containing complex / mitochondrion / membrane / cytosol / cytoplasm
Similarity search - Function
PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
STRONTIUM ION / Peroxisomal targeting signal 1 receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsStanley, W.A. / Wilmanns, M. / Kursula, P.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: A Previously Unobserved Conformation for the Human Pex5P Receptor Suggests Roles for Intrinsic Flexibility and Rigid Domain Motions in Ligand Binding
Authors: Stanley, W.A. / Pursiainen, N. / Garman, E.F. / Juffer, A. / Wilmanns, M. / Kursula, P.
History
DepositionNov 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
B: PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4334
Polymers72,2572
Non-polymers1752
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-82.9 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.670, 91.410, 119.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A463 - 639
2116B463 - 639
1126A315 - 442
2126B315 - 442

NCS ensembles :
ID
1
2

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Components

#1: Protein PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR / PEX5P / PEROXISOME RECEPTOR 1 / PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR / PTS1-BP / ...PEX5P / PEROXISOME RECEPTOR 1 / PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR / PTS1-BP / PEROXIN-5 / PTS1 RECEPTOR


Mass: 36128.691 Da / Num. of mol.: 2 / Fragment: TPR DOMAIN, RESIDUES 278-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50542
#2: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.35 Å3/Da / Density % sol: 39.53 %
Crystal growpH: 8.75
Details: 23% (W/V) PEG 3350, 100 MM TRIS-HCL (PH 8.75) AND 10 MM SRCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 16659 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C0M

2c0m


Resolution: 2.65→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.871 / SU B: 38.008 / SU ML: 0.372 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 834 5 %RANDOM
Rwork0.241 ---
obs0.244 15824 93.8 %-
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: 37.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--1.45 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4445 0 2 18 4465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224530
X-RAY DIFFRACTIONr_bond_other_d0.0010.023042
X-RAY DIFFRACTIONr_angle_refined_deg0.8761.9726146
X-RAY DIFFRACTIONr_angle_other_deg0.8137395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2255566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90924.227220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28315759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8631536
X-RAY DIFFRACTIONr_chiral_restr0.0490.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
X-RAY DIFFRACTIONr_nbd_refined0.1980.21223
X-RAY DIFFRACTIONr_nbd_other0.160.23284
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22237
X-RAY DIFFRACTIONr_nbtor_other0.0830.22424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1320.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.26122833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48134508
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.59841757
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.94651637
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

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12184loose positional0.985
21201loose positional1.845
12184loose thermal0.8210
21201loose thermal1.0610
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 60
Rwork0.3 1149
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)
110.38669.1001-6.268412.8058-8.411612.1185-0.47910.80290.2584-1.01160.58410.95640.0649-1.3874-0.105-0.07820.1715-0.1095-0.0344-0.09080.26462.51839.0596-6.2654
27.8593-1.36030.3325.30083.11772.0043-0.4346-0.2379-0.98481.71720.03421.35880.8313-0.79360.40040.1874-0.02050.23580.31030.06350.30221.0937-0.75315.0259
38.9609-2.42432.29459.3023-1.15613.7771-0.3999-0.3878-0.04520.16150.16210.54440.1021-0.30040.2378-0.06040.11070.0309-0.10510.0022-0.21469.16377.0397-0.8122
47.8197-3.44153.44951.806-1.05772.24910.0197-0.21620.5873-0.0592-0.0732-0.1413-0.63520.04660.05350.0481-0.0412-0.0014-0.11070.0065-0.138223.689611.8316-1.5809
51.82072.0412-1.06059.34360.50312.1127-0.31870.12750.1935-0.24-0.0173-0.4499-0.56440.33620.336-0.2058-0.048-0.064-0.15550.0107-0.098433.34563.1571-0.8784
65.34691.3401-1.98963.78850.30128.79030.09190.2955-0.6149-0.0182-0.141-0.26320.08610.02680.0491-0.36030.0253-0.0334-0.2728-0.0263-0.167724.7126-12.65-1.6961
77.8042.4278-1.09265.61793.211610.5684-0.2217-0.07840.04590.3848-0.02970.3318-0.0849-0.21550.2514-0.31590.0549-0.0551-0.33670.0231-0.225813.8599-18.9727-6.9979
83.70980.92471.14034.0401-3.89177.6914-0.05140.0040.2091-0.40690.07490.36790.0424-0.2872-0.0236-0.3258-0.0345-0.0194-0.23230.0163-0.12298.0386-23.5772-14.097
92.607-2.0158-0.356621.32293.5722.18550.59350.08620.50530.64360.2332-1.0423-0.27791.129-0.82670.4243-0.02670.1110.6872-0.10840.2127-14.2965-13.1693-30.4484
107.38162.98344.72092.5032.15795.5877-0.5206-0.26760.26570.16510.0440.0465-0.3678-0.1030.47670.03260.0034-0.1171-0.1804-0.0337-0.1259-6.9455-30.001-31.8741
116.58877.65134.103711.12381.14948.3972-0.98260.92650.9771-1.68640.75120.849-0.52220.0080.23140.0335-0.1662-0.12670.06140.1113-0.079810.1983-13.425-33.039
1211.26942.32961.38648.2857-0.28457.8425-0.3204-0.23951.0039-0.2367-0.02071.197-0.7666-0.00380.3411-0.0448-0.0525-0.0862-0.20230.01250.018718.1786-4.6768-22.7243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A312 - 335
2X-RAY DIFFRACTION2A336 - 366
3X-RAY DIFFRACTION3A367 - 399
4X-RAY DIFFRACTION4A400 - 442
5X-RAY DIFFRACTION5A466 - 519
6X-RAY DIFFRACTION5A1640
7X-RAY DIFFRACTION6A520 - 553
8X-RAY DIFFRACTION7A554 - 591
9X-RAY DIFFRACTION8A597 - 639
10X-RAY DIFFRACTION9B353 - 442
11X-RAY DIFFRACTION10B461 - 519
12X-RAY DIFFRACTION10B1640
13X-RAY DIFFRACTION11B520 - 593
14X-RAY DIFFRACTION12B594 - 639

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