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- PDB-4z9e: Alba from Thermoplasma volcanium -

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Basic information

Entry
Database: PDB / ID: 4z9e
TitleAlba from Thermoplasma volcanium
ComponentsDNA/RNA-binding protein Alba
KeywordsDNA BINDING PROTEIN / Thermoplasma volcanium / acetyltransferase
Function / homology
Function and homology information


chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA-binding protein Alba
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMa, C. / Lee, S.J. / Pathak, C. / Lee, B.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)20070056817 Korea, Republic Of
CitationJournal: Arch.Biochem.Biophys. / Year: 2016
Title: Alba from Thermoplasma volcanium belongs to alpha-NAT's: An insight into the structural aspects of Tv Alba and its acetylation by Tv Ard1.
Authors: Ma, C. / Pathak, C. / Lee, S.J. / Lee, K.Y. / Jang, S.B. / Nam, M. / Im, H. / Yoon, H.J. / Lee, B.J.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA-binding protein Alba
B: DNA/RNA-binding protein Alba
C: DNA/RNA-binding protein Alba
D: DNA/RNA-binding protein Alba


Theoretical massNumber of molelcules
Total (without water)44,2064
Polymers44,2064
Non-polymers00
Water72140
1
A: DNA/RNA-binding protein Alba
B: DNA/RNA-binding protein Alba


Theoretical massNumber of molelcules
Total (without water)22,1032
Polymers22,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area10060 Å2
MethodPISA
2
C: DNA/RNA-binding protein Alba
D: DNA/RNA-binding protein Alba


Theoretical massNumber of molelcules
Total (without water)22,1032
Polymers22,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-8 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.263, 84.248, 84.333
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
DNA/RNA-binding protein Alba


Mass: 11051.587 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) (archaea)
Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1
Gene: albA, TV1085, TVG1115434 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q979S5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 3350 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97953 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 20513 / % possible obs: 99.7 % / Redundancy: 7.6 % / Net I/σ(I): 43.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NFJ

1nfj


Resolution: 2.49→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.665 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23286 1050 5.1 %RANDOM
Rwork0.21268 ---
obs0.21371 19415 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.552 Å2
Baniso -1Baniso -2Baniso -3
1-8.08 Å2-0 Å20 Å2
2---3.75 Å20 Å2
3----4.34 Å2
Refinement stepCycle: 1 / Resolution: 2.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 0 40 2712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9583636
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29324.483116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68915528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8271520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021936
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 63 -
Rwork0.284 1232 -
obs--93.7 %

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