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- PDB-3vvt: Crystal structure of reconstructed archaeal ancestral NDK, Arc1 -

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Basic information

Entry
Database: PDB / ID: 3vvt
TitleCrystal structure of reconstructed archaeal ancestral NDK, Arc1
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / NDK / ARCHAEA / ANCESTOR
Function / homologyNucleoside diphosphate kinase-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNemoto, N. / Miyazono, K. / Kimura, M. / Yokobori, S. / Akanuma, S. / Tanokura, M. / Yamagishi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Experimental evidence for the thermophilicity of ancestral life
Authors: Akanuma, S. / Nakajima, Y. / Yokobori, S. / Kimura, M. / Nemoto, N. / Mase, T. / Miyazono, K. / Tanokura, M. / Yamagishi, A.
History
DepositionJul 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)31,2982
Polymers31,2982
Non-polymers00
Water75742
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)93,8956
Polymers93,8956
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.398, 110.398, 110.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 15649.168 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: There is no natural source since this sequence is estimated as archaeal ancestral NDK sequence by phylogenetic analysis. Host is Escherichia coli BL21(DE3) and plasmid is pET21c
References: nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.8M POTTASIUM SODIUM TARTRATE TETRAHYDRATE, 3% 2-METHYL-2,4,-PENTADIOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 17715 / % possible obs: 99.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 38.379
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.539 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cwk

2cwk


Resolution: 2.4→19.52 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.344 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 900 5.1 %RANDOM
Rwork0.186 ---
obs0.187 17682 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.28 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 0 42 2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9732988
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12323.26598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34915428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4541520
X-RAY DIFFRACTIONr_chiral_restr0.1580.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211654
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_it1.1351.51380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17822226
X-RAY DIFFRACTIONr_scbond_it4.1993848
X-RAY DIFFRACTIONr_scangle_it6.9914.5762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 54 -
Rwork0.259 1181 -
obs--97.63 %
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)
10.31840.2284-0.74630.8249-0.03372.26810.11420.1090.1240.053-0.01770.3087-0.2171-0.4239-0.09650.14360.06880.03870.2019-0.01940.128121.495-7.549-26.19
20.3520.1001-0.19460.8961-0.40461.31260.0119-0.01260.18380.14720.03890.1555-0.372-0.1139-0.05070.19480.0627-0.01510.09510.02080.134532.0454.79-46.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 139
2X-RAY DIFFRACTION2B1 - 139

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