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- PDB-6n2g: Crystal structure of Caenorhabditis elegans NAP1 -

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Basic information

Entry
Database: PDB / ID: 6n2g
TitleCrystal structure of Caenorhabditis elegans NAP1
ComponentsNucleosome Assembly Protein
KeywordsCHAPERONE / Nucleosome assembly / Histone binding
Function / homology
Function and homology information


somatic cell DNA recombination / cholesterol binding / nucleosome assembly / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin binding / chromatin / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsBhattacharyya, S. / DArcy, S.
CitationJournal: Biochemistry / Year: 2019
Title: Characterization of Caenorhabditis elegans Nucleosome Assembly Protein 1 Uncovers the Role of Acidic Tails in Histone Binding.
Authors: Sarkar, P. / Zhang, N. / Bhattacharyya, S. / Salvador, K. / D'Arcy, S.
History
DepositionNov 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleosome Assembly Protein
B: Nucleosome Assembly Protein
C: Nucleosome Assembly Protein
D: Nucleosome Assembly Protein


Theoretical massNumber of molelcules
Total (without water)142,8274
Polymers142,8274
Non-polymers00
Water00
1
A: Nucleosome Assembly Protein

D: Nucleosome Assembly Protein


Theoretical massNumber of molelcules
Total (without water)71,4132
Polymers71,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area8530 Å2
ΔGint-61 kcal/mol
Surface area28860 Å2
MethodPISA
2
B: Nucleosome Assembly Protein
C: Nucleosome Assembly Protein


Theoretical massNumber of molelcules
Total (without water)71,4132
Polymers71,4132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-61 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.597, 154.868, 92.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 13 through 250 or (resid 251...
21(chain B and (resid 13 through 91 or (resid 92...
31(chain C and (resid 13 through 91 or (resid 92...
41(chain D and (resid 13 through 91 or (resid 92...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYS(chain A and (resid 13 through 250 or (resid 251...AA13 - 25013 - 250
12ASPASPASPASP(chain A and (resid 13 through 250 or (resid 251...AA251251
13GLYGLYPHEPHE(chain A and (resid 13 through 250 or (resid 251...AA10 - 29810 - 298
14GLYGLYPHEPHE(chain A and (resid 13 through 250 or (resid 251...AA10 - 29810 - 298
15GLYGLYPHEPHE(chain A and (resid 13 through 250 or (resid 251...AA10 - 29810 - 298
16GLYGLYPHEPHE(chain A and (resid 13 through 250 or (resid 251...AA10 - 29810 - 298
21SERSERGLYGLY(chain B and (resid 13 through 91 or (resid 92...BB13 - 9113 - 91
22LEULEULEULEU(chain B and (resid 13 through 91 or (resid 92...BB9292
23SERSERGLNGLN(chain B and (resid 13 through 91 or (resid 92...BB13 - 29313 - 293
24SERSERGLNGLN(chain B and (resid 13 through 91 or (resid 92...BB13 - 29313 - 293
25SERSERGLNGLN(chain B and (resid 13 through 91 or (resid 92...BB13 - 29313 - 293
26SERSERGLNGLN(chain B and (resid 13 through 91 or (resid 92...BB13 - 29313 - 293
31SERSERGLYGLY(chain C and (resid 13 through 91 or (resid 92...CC13 - 9113 - 91
32LEULEULEULEU(chain C and (resid 13 through 91 or (resid 92...CC9292
33GLYGLYPHEPHE(chain C and (resid 13 through 91 or (resid 92...CC10 - 29810 - 298
34GLYGLYPHEPHE(chain C and (resid 13 through 91 or (resid 92...CC10 - 29810 - 298
35GLYGLYPHEPHE(chain C and (resid 13 through 91 or (resid 92...CC10 - 29810 - 298
36GLYGLYPHEPHE(chain C and (resid 13 through 91 or (resid 92...CC10 - 29810 - 298
41SERSERGLYGLY(chain D and (resid 13 through 91 or (resid 92...DD13 - 9113 - 91
42LEULEULEULEU(chain D and (resid 13 through 91 or (resid 92...DD9292
43SERSERGLNGLN(chain D and (resid 13 through 91 or (resid 92...DD13 - 29313 - 293
44SERSERGLNGLN(chain D and (resid 13 through 91 or (resid 92...DD13 - 29313 - 293
45SERSERGLNGLN(chain D and (resid 13 through 91 or (resid 92...DD13 - 29313 - 293
46SERSERGLNGLN(chain D and (resid 13 through 91 or (resid 92...DD13 - 29313 - 293

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Components

#1: Protein
Nucleosome Assembly Protein


Mass: 35706.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nap-1, CELE_D2096.8, D2096.8 / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q19007

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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: 3.43 Å3/Da / Density % sol: 64.16 % / Mosaicity: 0.53 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Sodium HEPES pH 7.5 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.003→154.868 Å / Num. obs: 61500 / % possible obs: 89.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 56.33 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Rsym value: 0.115 / Net I/av σ(I): 6.1 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.003-3.176.80.6661.251410.270.720.66697.4
3.17-3.367.40.3562.250010.140.3830.356100
3.36-3.596.40.292.632550.1240.3160.2969
3.59-3.8860.2232.731000.1030.2470.22370.6
3.88-4.2570.1047.332530.0430.1130.10479.9
4.25-4.757.30.0819.337000.0320.0870.081100
4.75-5.487.30.07210.232950.0290.0780.072100
5.48-6.717.20.077928050.0310.0830.077100
6.71-9.570.04314.122090.0170.0460.043100
9.5-19.7966.60.02816.311360.0120.030.02888.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.003→19.796 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.82 / Phase error: 27.3
RfactorNum. reflection% reflection
Rfree0.2553 3787 6.16 %
Rwork0.2407 --
obs0.2416 61500 88.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.01 Å2 / Biso mean: 56.5533 Å2 / Biso min: 27.61 Å2
Refinement stepCycle: final / Resolution: 3.003→19.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8866 0 0 0 8866
Num. residues----1112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049052
X-RAY DIFFRACTIONf_angle_d0.72112223
X-RAY DIFFRACTIONf_chiral_restr0.0441349
X-RAY DIFFRACTIONf_plane_restr0.0051592
X-RAY DIFFRACTIONf_dihedral_angle_d2.6055491
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5333X-RAY DIFFRACTION10.107TORSIONAL
12B5333X-RAY DIFFRACTION10.107TORSIONAL
13C5333X-RAY DIFFRACTION10.107TORSIONAL
14D5333X-RAY DIFFRACTION10.107TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0027-3.04060.34341940.36351972216686
3.0406-3.08040.32091790.341624032582100
3.0804-3.12250.487180.3325372555100
3.1225-3.16690.3061950.320823802575100
3.1669-3.2140.33531940.302623712565100
3.214-3.2640.35381920.299123672559100
3.264-3.31730.29361920.299824032595100
3.3173-3.3742100000000.28892541100
3.3742-3.43520.34221900.3131194138485
3.4352-3.5009100000000.294579782
3.5009-3.5720.27181960.26962372256899
3.572-3.64920.32511870.30241910209791
3.6492-3.7335100000000.257464885
3.7335-3.82630.32911870.27272365255299
3.8263-3.9289100000000.303696986
3.9289-4.04360.2761900.24852041223195
4.0436-4.17290.22271850.2222372255799
4.1729-4.3206100000000.21412547100
4.3206-4.49170.20681940.20423572551100
4.4917-4.69350.24051830.20672383256699
4.6935-4.93730.20711850.19623552540100
4.9373-5.24130.24891860.210124002586100
5.2413-5.63730.2421920.21432342253499
5.6373-6.1888100000000.22322590100
6.1888-7.04870.23251900.22152366255699
7.0487-8.75110.20851840.1923662550100
8.7511-19.79680.17561740.18512365253999
Refinement TLS params.Method: refined / Origin x: -0.5427 Å / Origin y: 32.7945 Å / Origin z: 0.3781 Å
111213212223313233
T0.3743 Å2-0.0273 Å20.0072 Å2-0.3328 Å20.0259 Å2--0.3674 Å2
L0.04 °2-0.0456 °20.1035 °2--0.042 °2-0.0446 °2--0.42 °2
S-0.0436 Å °0.0334 Å °0.0099 Å °0.0391 Å °-0.0077 Å °0.0302 Å °-0.1552 Å °0.0147 Å °0.0482 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 298
2X-RAY DIFFRACTION1allB13 - 293
3X-RAY DIFFRACTION1allC10 - 298
4X-RAY DIFFRACTION1allD13 - 293

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