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- PDB-1u2h: X-ray Structure of the N-terminally truncated human APEP-1 -

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Basic information

Entry
Database: PDB / ID: 1u2h
TitleX-ray Structure of the N-terminally truncated human APEP-1
ComponentsAortic preferentially expressed protein 1
KeywordsCONTRACTILE PROTEIN / Structural Genomics / Ig-fold I-set / RGD motif / Homophilic Adhesion / Arterial Smooth Muscle Cells / Atherosclerosis
Function / homology
Function and homology information


muscle cell differentiation / muscle organ development / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
Unstructured region on SPEG complex protein / : / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Unstructured region on SPEG complex protein / : / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Striated muscle preferentially expressed protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsManjasetty, B.A. / Scheich, C. / Roske, Y. / Niesen, F.H. / Gotz, F. / Bussow, K. / Heinemann, U.
CitationJournal: Bmc Struct.Biol. / Year: 2005
Title: X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1)
Authors: Manjasetty, B.A. / Niesen, F.H. / Scheich, C. / Roske, Y. / Gotz, F. / Behlke, J. / Sievert, V. / Heinemann, U. / Bussow, K.
History
DepositionJul 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Aortic preferentially expressed protein 1


Theoretical massNumber of molelcules
Total (without water)11,1371
Polymers11,1371
Non-polymers00
Water2,702150
1
A: Aortic preferentially expressed protein 1

A: Aortic preferentially expressed protein 1


Theoretical massNumber of molelcules
Total (without water)22,2732
Polymers22,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)81.541, 25.522, 42.544
Angle α, β, γ (deg.)90.00, 104.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aortic preferentially expressed protein 1 / APEG-1


Mass: 11136.670 Da / Num. of mol.: 1 / Fragment: residues 15-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PSF CLONE ID 111408 and RZPD ID PSFEp250B117 / Gene: Arotic Preferentially Expressed Gene 1 / Plasmid: pRARE / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1 / References: UniProt: Q15772
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.8 Å3/Da / Density % sol: 32.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG MME 2000, 200mM (NH4)2SO4, 100mM Na Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 2004 / Details: mirrors
RadiationMonochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.96→20 Å / Num. all: 183130 / Num. obs: 46733 / % possible obs: 89.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 29.9
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1651 / Rsym value: 0.16 / % possible all: 47.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6)

1fhg

1bih

1cs6


Resolution: 0.96→5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.569 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17213 2384 5.1 %RANDOM
Rwork0.16053 ---
obs0.16113 43956 89.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0.38 Å2
2--0.58 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 0.96→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms766 0 0 150 916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022778
X-RAY DIFFRACTIONr_bond_other_d0.0020.02733
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9541046
X-RAY DIFFRACTIONr_angle_other_deg331693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.654595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67621.90542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53415140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4181514
X-RAY DIFFRACTIONr_chiral_restr0.0990.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02173
X-RAY DIFFRACTIONr_nbd_refined0.2170.2116
X-RAY DIFFRACTIONr_nbd_other0.2170.2740
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2354
X-RAY DIFFRACTIONr_nbtor_other0.0880.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.230
X-RAY DIFFRACTIONr_mcbond_it1.9171.5513
X-RAY DIFFRACTIONr_mcbond_other0.6711.5196
X-RAY DIFFRACTIONr_mcangle_it2.3872767
X-RAY DIFFRACTIONr_scbond_it2.943324
X-RAY DIFFRACTIONr_scangle_it3.8084.5279
X-RAY DIFFRACTIONr_rigid_bond_restr1.30231667
X-RAY DIFFRACTIONr_sphericity_free8.0133152
X-RAY DIFFRACTIONr_sphericity_bonded3.15731499
LS refinement shellResolution: 0.96→0.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 96 -
Rwork0.212 1699 -
obs--48.49 %

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