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- PDB-2q8k: The crystal structure of Ebp1 -

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Basic information

Entry
Database: PDB / ID: 2q8k
TitleThe crystal structure of Ebp1
ComponentsProliferation-associated protein 2G4
KeywordsTRANSCRIPTION / Ebp1 / PA2G4 / Methionine Aminopeptidase / pita-bread
Function / homology
Function and homology information


positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / azurophil granule lumen / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation ...positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / azurophil granule lumen / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / negative regulation of apoptotic process / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm
Similarity search - Function
PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proliferation-associated protein 2G4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKowalinski, E. / Bange, G. / Wild, K. / Sinning, I.
CitationJournal: Febs Lett. / Year: 2007
Title: The crystal structure of Ebp1 reveals a methionine aminopeptidase fold as binding platform for multiple interactions.
Authors: Kowalinski, E. / Bange, G. / Bradatsch, B. / Hurt, E. / Wild, K. / Sinning, I.
History
DepositionJun 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferation-associated protein 2G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4028
Polymers44,7381
Non-polymers6657
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.887, 73.887, 183.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Proliferation-associated protein 2G4 / Cell cycle protein p38-2G4 homolog / hG4-1 / ErbB3-binding protein 1


Mass: 44737.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PA2G4, EBP1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UQ80
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.3 M Ammoniumsulfate, 0.1M Citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2006 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→68 Å / Num. obs: 67896 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rsym value: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.407 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKM.pdb

1wkm


Resolution: 1.6→57.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.974 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21852 3451 5.1 %RANDOM
Rwork0.18235 ---
obs0.18416 64263 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.6→57.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 37 487 3288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9733956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63825.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7071512
X-RAY DIFFRACTIONr_chiral_restr0.090.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022167
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21404
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22010
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2031.51875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7522933
X-RAY DIFFRACTIONr_scbond_it2.95631166
X-RAY DIFFRACTIONr_scangle_it3.7524.51014
X-RAY DIFFRACTIONr_rigid_bond_restr2.48133041
X-RAY DIFFRACTIONr_sphericity_free4.3313487
X-RAY DIFFRACTIONr_sphericity_bonded4.25132874
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 256 -
Rwork0.245 4687 -
obs--100 %

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