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- PDB-4xul: Crystal structure of M. chilensis Mg662 protein complexed with GTP -

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Basic information

Entry
Database: PDB / ID: 4xul
TitleCrystal structure of M. chilensis Mg662 protein complexed with GTP
Componentsmg662
KeywordsTRANSFERASE / nucleotidyl transferase / GTP complex / ORFan
Function / homology: / : / L544, nucleotidyltransferase domain / Nucleotidyl transferase L544, helical domain / GTP binding / metal ion binding / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein mg662
Function and homology information
Biological speciesMegavirus chiliensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsLartigue, A. / Priet, S. / Claverie, J.M. / Abergel, C.
CitationJournal: To Be Published
Title: Crystal structure of M. chilensis Mg662 protein complexed with GTP
Authors: Lartigue, A. / Priet, S. / Claverie, J.M. / Abergel, C.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mg662
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7615
Polymers46,1661
Non-polymers5954
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-34 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.360, 99.360, 168.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein mg662


Mass: 46165.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megavirus chiliensis / Gene: mg662 / Plasmid: MODIFIED PETDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: G5CQN7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 4.53 Å3/Da / Density % sol: 72.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Protein concentration: 5-12 mg/mL in 10 mM CAPS, 150 mM NaCl, pH 10.5 Reservoir solution: 0.05 M MES, 0.08 M Ammonium acetate pH 6.4 Soaking 0.5 mM GTP, UV treatment 5 minutes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.26→168.99 Å / Num. obs: 40442 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 54.56 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.037 / Net I/σ(I): 13 / Num. measured all: 529090
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
2.26-2.6113.30.6894184276139060.9330.195
4.52-168.9912.20.109246583553900.990.033

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.5data scaling
PHASER2.5.6phasing
XDSdata reduction
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4AMS

4ams


Resolution: 2.26→38.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 2017 5 %
Rwork0.1908 38331 -
obs0.1922 40348 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.14 Å2 / Biso mean: 62.9484 Å2 / Biso min: 35.05 Å2
Refinement stepCycle: final / Resolution: 2.26→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 35 211 3300
Biso mean--55.55 68.48 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033155
X-RAY DIFFRACTIONf_angle_d0.7524278
X-RAY DIFFRACTIONf_chiral_restr0.028469
X-RAY DIFFRACTIONf_plane_restr0.004534
X-RAY DIFFRACTIONf_dihedral_angle_d12.7521206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2601-2.31660.28431350.270226832818
2.3166-2.37920.31211390.254926862825
2.3792-2.44920.28641280.240126952823
2.4492-2.52820.24441340.225627002834
2.5282-2.61860.29351190.220527372856
2.6186-2.72340.23231530.215126682821
2.7234-2.84730.21591540.218127192873
2.8473-2.99740.25221500.22227052855
2.9974-3.18510.25131530.208327132866
3.1851-3.43090.24021430.204327472890
3.4309-3.77590.21351420.190127392881
3.7759-4.32160.19291620.167527652927
4.3216-5.44240.17051500.16128062956
5.4424-38.88540.21641550.180929683123

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