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- PDB-3hfd: Nucleosome Assembly Protein 1 from Plasmodium knowlesi -

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Basic information

Entry
Database: PDB / ID: 3hfd
TitleNucleosome Assembly Protein 1 from Plasmodium knowlesi
ComponentsNucleosome assembly protein 1
KeywordsCHAPERONE / PROTEIN TRANSPORT / histone binding / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


nucleosome assembly / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Nucleosome assembly protein / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Arylsulfatase, C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nucleosome assembly protein, putative / Nucleosome assembly protein, putative
Similarity search - Component
Biological speciesPlasmodium knowlesi strain H (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsArakaki, T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: To be Published
Title: Nucleosome Assembly Protein 1 from Plasmodium knowlesi
Authors: Merritt, E.A. / Arakaki, T. / Napuli, A. / Mueller, N. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, L.M.J. / Zhang, L. / Hol, W.G.J.
History
DepositionMay 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleosome assembly protein 1


Theoretical massNumber of molelcules
Total (without water)32,4881
Polymers32,4881
Non-polymers00
Water23413
1
A: Nucleosome assembly protein 1

A: Nucleosome assembly protein 1


Theoretical massNumber of molelcules
Total (without water)64,9762
Polymers64,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4020 Å2
ΔGint-33 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.895, 38.259, 80.477
Angle α, β, γ (deg.)90.000, 100.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleosome assembly protein 1


Mass: 32487.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cleaved
Source: (gene. exp.) Plasmodium knowlesi strain H (eukaryote)
Gene: PKH_130240 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3LB24, UniProt: A0A384KYS3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1 M NaCl, 0.1 M Tris, 32% PEG 3350, pH 8.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→79.06 Å / Num. obs: 5581 / % possible obs: 95.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.035 / Net I/σ(I): 16.551
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.92.70.2144390.977177.2
2.9-3.022.90.1975020.96186.4
3.02-3.153.10.1565441.002194.1
3.15-3.323.40.1395761.069198.3
3.32-3.533.50.1285691.082199.6
3.53-3.83.60.0895711.0951100
3.8-4.183.60.0755871.0211100
4.18-4.783.70.0565971.0181100
4.78-6.023.60.0455791.056199.8
6.02-303.40.0316171.011199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0089refinement
PDB_EXTRACT3.005data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.806 / Occupancy max: 1 / Occupancy min: 1 / SU B: 48.123 / SU ML: 0.415 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.55 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.328 255 4.6 %RANDOM
Rwork0.225 ---
obs0.23 5580 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.81 Å2 / Biso mean: 23.885 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-1.93 Å2
2--3.3 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 13 1793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221823
X-RAY DIFFRACTIONr_bond_other_d0.0010.021219
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.952468
X-RAY DIFFRACTIONr_angle_other_deg0.81932965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3765209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33224.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11815310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.941158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_mcbond_it0.3391.51066
X-RAY DIFFRACTIONr_mcbond_other0.0421.5426
X-RAY DIFFRACTIONr_mcangle_it0.65921726
X-RAY DIFFRACTIONr_scbond_it0.8533757
X-RAY DIFFRACTIONr_scangle_it1.5024.5742
LS refinement shellResolution: 2.8→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 12 -
Rwork0.282 323 -
all-335 -
obs--74.78 %
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)
12.8828-1.36595.0940.7283-2.39159.61930.0333-0.15720.01670.05540.12070.0250.0321-0.2204-0.1540.1023-0.04050.01540.23680.00240.1661-12.418-13.334-12.073
23.8164-1.8106-0.8658.03043.65385.6410.0062-0.04850.26360.37460.12410.1460.03640.4178-0.13030.0809-0.0277-0.01080.3711-0.03810.05928.544-2.07125.599
38.90193.03318.17633.89063.93919.01430.34730.18420.04490.1195-0.52020.47480.9157-0.11790.17290.3565-0.0367-0.0180.2903-0.0240.2167-2.471-6.02520.655
45.32651.14982.87132.24552.32627.60440.11880.3759-0.3013-0.2899-0.0770.34310.0901-0.3158-0.04180.11990.0235-0.10560.2421-0.00720.1265-5.8332.07224.86
51.9915-4.4014-1.193810.46392.34710.83780.1022-0.15470.12710.053-0.052-0.2764-0.22030.2282-0.05020.532-0.0623-0.00170.3781-0.0210.4669-2.51320.20834.489
67.73312.40333.926314.08238.72366.2287-0.2380.0073-0.05080.1050.4426-0.298-0.03330.2625-0.20460.0905-0.0057-0.00190.15580.04220.0503-1.5349.40623.333
73.0631-3.8784.40774.9459-5.80728.0970.0217-0.1960.4604-0.11220.2426-0.44750.36-0.9053-0.26430.5522-0.006-0.19190.80910.12260.5847-8.26311.45711.425
813.5676-2.49041.91321.7235-0.24431.92830.0050.58040.2259-0.26560.0352-0.08190.05040.2033-0.04020.14280.0077-0.02840.16050.00430.107310.026-2.12914.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 72
2X-RAY DIFFRACTION2A73 - 126
3X-RAY DIFFRACTION3A127 - 145
4X-RAY DIFFRACTION4A146 - 193
5X-RAY DIFFRACTION5A194 - 222
6X-RAY DIFFRACTION6A223 - 229
7X-RAY DIFFRACTION7A230 - 262
8X-RAY DIFFRACTION8A263 - 281

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