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- PDB-1nlq: The crystal structure of Drosophila NLP-core provides insight int... -

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Basic information

Entry
Database: PDB / ID: 1nlq
TitleThe crystal structure of Drosophila NLP-core provides insight into pentamer formation and histone binding
ComponentsNucleoplasmin-like protein
KeywordsCHAPERONE / LIGAND BINDING / dNLP / Nucleoplasmin / histone binding
Function / homology
Function and homology information


TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / sperm DNA decondensation / SUMOylation of transcription cofactors / histone binding / chromatin remodeling / chromatin binding / nucleolus / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nucleoplasmin-like protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsNamboodiri, V.M.H. / Dutta, S. / Akey, I.V. / Head, J.F. / Akey, C.W.
CitationJournal: Structure / Year: 2003
Title: The crystal structure of Drosophila NLP-core Provides Insight into Pentamer Formation and Histone Binding
Authors: Namboodiri, V.M.H. / Dutta, S. / Akey, I.V. / Head, J.F. / Akey, C.W.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_id / _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_asym_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Nucleoplasmin-like protein
B: Nucleoplasmin-like protein
C: Nucleoplasmin-like protein
D: Nucleoplasmin-like protein
E: Nucleoplasmin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9017
Polymers59,8525
Non-polymers492
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-57 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.608, 60.089, 73.426
Angle α, β, γ (deg.)90.00, 90.79, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a pentamer

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Components

#1: Protein
Nucleoplasmin-like protein / dNLP / Chromatin decondensation protein 1


Mass: 11970.385 Da / Num. of mol.: 5 / Fragment: N-Terminal core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: NLP OR CRP1 OR CG7917 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q27415
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, sodium chloride, magnesium chloride, tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
230-33 %PEG4001reservoir
320 mM1reservoirMgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9795
SYNCHROTRONNSLS X8C20.919997, 0.916998, 0.919781
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2001 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.9199971
30.9169981
40.9197811
ReflectionResolution: 1.5→50 Å / Num. all: 80828 / Num. obs: 80828 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.037 / Rsym value: 0.029 / Net I/σ(I): 39.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 6.7 / Num. unique all: 437 / Rsym value: 0.253 / % possible all: 94.5
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 478081 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 94.5 % / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→31.15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 6207 -Random
Rwork0.234 ---
all0.237 80330 --
obs-76420 87.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-1.36 Å20.12 Å2
2--0 Å2-0.09 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 2 358 4147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.294 --
Rwork0.314 --
obs-10924 89.6 %
Refinement
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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