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- PDB-5day: The structure of NAP1-Related Protein(NRP1) in Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 5day
TitleThe structure of NAP1-Related Protein(NRP1) in Arabidopsis
ComponentsNAP1-related protein 1
KeywordsCHAPERONE / histone chaperone / NAP1-Related protein / transcriptional activation
Function / homology
Function and homology information


somatic cell DNA recombination / double-strand break repair via homologous recombination / nucleosome assembly / histone binding / chromatin binding / chromatin / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Arylsulfatase, C-terminal domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NAP1-related protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.329 Å
AuthorsZhu, Y. / Rong, L. / Yang, Y. / Zhang, C. / Feng, H.Y. / Zheng, L.N. / Shen, W.H. / Ma, J.B. / Dong, A.W.
CitationJournal: To Be Published
Title: The structure of NAP1-Related Protein(NRP1) in Arabidopsis
Authors: Zhu, Y. / Rong, L. / Yang, Y. / Zhang, C. / Feng, H.Y. / Zheng, L.N. / Shen, W.H. / Ma, J.B. / Dong, A.W.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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 / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAP1-related protein 1
B: NAP1-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1065
Polymers47,9852
Non-polymers1203
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-47 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.542, 60.812, 135.248
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAP1-related protein 1 / Nucleosome/chromatin assembly factor group A6 / Protein SET homolog 1


Mass: 23992.643 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NRP1, NFA6, At1g74560, F1M20.24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CA59
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.58 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 25% PEG 400, 0.1 M HEPES pH 7.6, 0.2 M Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97900, 0.97946, 0.97930, 0.95365
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979461
30.97931
40.953651
ReflectionResolution: 2.329→50 Å / Num. obs: 21817 / % possible obs: 99.5 % / Redundancy: 6 % / Rsym value: 0.055 / Net I/σ(I): 43.7
Reflection shellResolution: 2.33→2.41 Å / Num. unique all: 1969

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Processing

Software
NameVersionClassification
PHENIX1.10_2152refinement
HKL-2000data reduction
Cootdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.329→45.218 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 27.14 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2688 2004 9.2 %
Rwork0.23 --
obs0.2336 21784 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.329→45.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 3 101 2945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072903
X-RAY DIFFRACTIONf_angle_d0.8333928
X-RAY DIFFRACTIONf_dihedral_angle_d12.4681730
X-RAY DIFFRACTIONf_chiral_restr0.048440
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3293-2.38750.32831390.26681339X-RAY DIFFRACTION96
2.3875-2.45210.32131380.24781404X-RAY DIFFRACTION100
2.4521-2.52420.31431470.24461417X-RAY DIFFRACTION99
2.5242-2.60570.35951360.25271379X-RAY DIFFRACTION99
2.6057-2.69880.31651440.26031389X-RAY DIFFRACTION99
2.6988-2.80680.26941400.24331407X-RAY DIFFRACTION100
2.8068-2.93460.30491440.24751395X-RAY DIFFRACTION100
2.9346-3.08930.30931450.25141432X-RAY DIFFRACTION100
3.0893-3.28280.29831410.24641402X-RAY DIFFRACTION100
3.2828-3.53610.27371460.2231433X-RAY DIFFRACTION100
3.5361-3.89180.23951460.21421430X-RAY DIFFRACTION100
3.8918-4.45450.20391480.2061441X-RAY DIFFRACTION99
4.4545-5.61060.24291430.20531436X-RAY DIFFRACTION98
5.6106-45.22620.28211470.24271476X-RAY DIFFRACTION95
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)
10.2035-0.1058-0.79420.6969-0.98653.3861-0.1030.07890.15610.2099-0.0277-0.3475-0.63620.0580.17990.3138-0.1058-0.02940.3534-0.03290.412412.66392.601421.3343
23.22480.50050.05094.5292-0.13242.1361-0.12840.32570.4570.13880.1672-1.0129-0.48210.82-0.05640.4227-0.1435-0.06230.70440.01690.648521.5526-0.405135.5062
30.75730.3769-0.7871.0095-2.22234.2522-0.09770.21690.0047-0.230.0655-0.24950.2588-0.14970.05210.5191-0.01860.06290.2944-0.07430.364611.7825-1.90717.6595
45.1762-0.0514-0.50883.73830.51273.1769-0.41970.1638-0.66150.24610.2736-0.52090.73790.15510.1720.84880.04190.13890.4292-0.04550.533218.327-3.5404-4.7197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 224 )
3X-RAY DIFFRACTION3chain 'B' and (resid 18 through 113 )
4X-RAY DIFFRACTION4chain 'B' and (resid 114 through 225 )

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