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- PDB-6k02: Crystal structure of ceNAP1 core -

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Basic information

Entry
Database: PDB / ID: 6k02
TitleCrystal structure of ceNAP1 core
ComponentsNucleosome Assembly Protein
KeywordsCHAPERONE / NAP1
Function / homology
Function and homology information


cholesterol binding / double-strand break repair via homologous recombination / nucleosome assembly / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin binding / chromatin / metal ion binding / nucleus / 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: 2.162 Å
AuthorsLiu, Y.R.
CitationJournal: Structure / Year: 2019
Title: Crystal structure of xlH2A-H2B
Authors: Liu, Y.R.
History
DepositionMay 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1094
Polymers69,9782
Non-polymers1312
Water1,09961
1
A: Nucleosome Assembly Protein
hetero molecules

A: Nucleosome Assembly Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1094
Polymers69,9782
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9280 Å2
ΔGint-133 kcal/mol
Surface area25420 Å2
MethodPISA
2
B: Nucleosome Assembly Protein
hetero molecules

B: Nucleosome Assembly Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1094
Polymers69,9782
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9380 Å2
ΔGint-128 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.733, 126.747, 118.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 294)
21(chain B and (resid 4 through 12 or (resid 13...

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
11LEULEUSERSER(chain A and resid 4 through 294)AA4 - 29416 - 306
21LEULEULEULEU(chain B and (resid 4 through 12 or (resid 13...BB4 - 1216 - 24
22SERSERSERSER(chain B and (resid 4 through 12 or (resid 13...BB1325
23LEULEUASPASP(chain B and (resid 4 through 12 or (resid 13...BB4 - 29516 - 307
24LEULEUASPASP(chain B and (resid 4 through 12 or (resid 13...BB4 - 29516 - 307
25LEULEUASPASP(chain B and (resid 4 through 12 or (resid 13...BB4 - 29516 - 307
26LEULEUASPASP(chain B and (resid 4 through 12 or (resid 13...BB4 - 29516 - 307

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Components

#1: Protein Nucleosome Assembly Protein


Mass: 34989.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nap-1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q19007
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Zinc acetate dihydrate, 0.1M Sodium cacodylate tridydrate pH=6.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.16→37.2 Å / Num. obs: 38052 / % possible obs: 99.2 % / Redundancy: 9.9 % / Net I/σ(I): 20
Reflection shellResolution: 2.16→2.24 Å / Rmerge(I) obs: 0.845 / Num. unique obs: 38052

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.162→37.196 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.37
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2792 1945 5.11 %
Rwork0.2502 --
obs0.2517 38052 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.95 Å2 / Biso mean: 31.4855 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 2.162→37.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 2 61 4299
Biso mean--19.58 24.45 -
Num. residues----532
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1568X-RAY DIFFRACTION5.618TORSIONAL
12B1568X-RAY DIFFRACTION5.618TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1621-2.21620.32671190.25712349246890
2.2162-2.27610.2517970.26512636273399
2.2761-2.34310.291400.2542573271399
2.3431-2.41870.27781450.2652455260095
2.4187-2.50510.30761270.26832585271299
2.5051-2.60540.31471430.269325802723100
2.6054-2.72390.30591460.269626012747100
2.7239-2.86750.29611550.273725902745100
2.8675-3.04710.31961420.27526282770100
3.0471-3.28220.28651530.263125992752100
3.2822-3.61230.28521440.23672540268497
3.6123-4.13440.2051260.218926592785100
4.1344-5.20660.2491490.211326632812100
5.2066-37.20120.29991590.27162649280896
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.10220.21380.57851.0459-0.06920.29540.074-0.203-0.03850.1546-0.0762-0.159-0.0537-0.07210.0010.21820.0188-0.0230.13940.00940.10599.4314-38.651538.4176
21.6518-0.2698-0.8961.02310.06750.69390.04060.15590.0131-0.1489-0.007-0.1069-0.0367-0.0635-0.04070.1987-0.01960.01670.13550.00080.11148.7181-8.807519.4377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 294)A3 - 294
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 295)B4 - 295

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