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- PDB-2q98: X-ray structure of a prolactin antagonist -

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Basic information

Entry
Database: PDB / ID: 2q98
TitleX-ray structure of a prolactin antagonist
ComponentsProlactin
KeywordsHORMONE / antagonist receptor interaction
Function / homology
Function and homology information


prolactin receptor binding / positive regulation of lactation / prolactin signaling pathway / mammary gland development / Prolactin receptor signaling / negative regulation of endothelial cell proliferation / Growth hormone receptor signaling / lactation / negative regulation of angiogenesis / response to nutrient levels ...prolactin receptor binding / positive regulation of lactation / prolactin signaling pathway / mammary gland development / Prolactin receptor signaling / negative regulation of endothelial cell proliferation / Growth hormone receptor signaling / lactation / negative regulation of angiogenesis / response to nutrient levels / endosome lumen / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / positive regulation of miRNA transcription / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / Amyloid fiber formation / positive regulation of cell population proliferation / extracellular space / extracellular region
Similarity search - Function
Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBroutin, I.J.L. / Ducruix, A. / Jomain, J.B. / Goffin, V.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and thermodynamic bases for the design of pure prolactin receptor antagonists: X-ray structure of Del1-9-G129R-hPRL.
Authors: Jomain, J.B. / Tallet, E. / Broutin, I. / Hoos, S. / van Agthoven, J. / Ducruix, A. / Kelly, P.A. / Kragelund, B.B. / England, P. / Goffin, V.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prolactin


Theoretical massNumber of molelcules
Total (without water)22,3651
Polymers22,3651
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.590, 122.590, 28.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a monomer

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Components

#1: Protein Prolactin / PRL


Mass: 22364.520 Da / Num. of mol.: 1 / Mutation: C39S,G157R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRL / Plasmid: pQE70 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01236
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 675 mM K2HPO4, 45 mM (NH4)2PO4, 50 mM LiSO4, 7.5 % glycerol, 8% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979989 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2006 / Details: mirror
RadiationMonochromator: Si 111 & 311 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979989 Å / Relative weight: 1
ReflectionResolution: 2.6→86.711 Å / Num. obs: 6433 / % possible obs: 93.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 44.357 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.742.40.2352.822169050.23593.1
2.74-2.912.40.1943.520658500.19490.1
2.91-3.112.40.1414.520218320.14196.2
3.11-3.362.50.1016.119237790.10195.6
3.36-3.682.50.079.518467480.0795.8
3.68-4.112.50.06110.116106520.06193.8
4.11-4.752.40.0679.313715830.06796.4
4.75-5.812.40.0658.311494770.06591.5
5.81-8.222.30.0639.38983950.06395.6
8.22-86.712.30.069.24842120.0685.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å61.29 Å
Translation2.6 Å61.29 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F6F CHAIN A

1f6f


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.831 / SU B: 16.262 / SU ML: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.302 632 11 %RANDOM
Rwork0.211 ---
obs0.221 5771 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 0 48 1615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211598
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9572158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.24823.95181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.21115302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4581513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021198
X-RAY DIFFRACTIONr_nbd_refined0.2320.2789
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.28
X-RAY DIFFRACTIONr_mcbond_it0.7051.5982
X-RAY DIFFRACTIONr_mcangle_it1.28821554
X-RAY DIFFRACTIONr_scbond_it1.73674
X-RAY DIFFRACTIONr_scangle_it2.8594.5604
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 49 -
Rwork0.29 375 -
obs-424 100 %

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