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- PDB-2yxh: Crystal structure of mazG-related protein from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 2yxh
TitleCrystal structure of mazG-related protein from Thermotoga maritima
ComponentsMazG-related protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TM0360 / Left-handed superhelix fold / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


TTP catabolic process / UTP catabolic process / dTTP catabolic process / nucleoside triphosphate diphosphatase activity / dATP catabolic process / dUTP catabolic process / dGTP catabolic process / metal ion binding
Similarity search - Function
NTP pyrophosphohydrolase MazG / : / NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MazG-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsPadmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of mazG-related protein from Thermotoga maritima
Authors: Padmanabhan, B. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MazG-related protein
B: MazG-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5086
Polymers27,4112
Non-polymers974
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-87 kcal/mol
Surface area11830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.829, 56.788, 61.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-586-

HOH

21B-611-

HOH

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Components

#1: Protein MazG-related protein


Mass: 13705.542 Da / Num. of mol.: 2 / Mutation: L57MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL-X / References: UniProt: Q9WYJ5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 25% PEG3350, 0.2M MgAcetate, 0.1M Tris-HCl, pH8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97905, 0.90000, 0.97945
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.91
30.979451
ReflectionResolution: 2→50 Å / Num. all: 18461 / Num. obs: 18408 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.258 / Num. unique all: 1765 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.62 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26312 930 5.1 %RANDOM
Rwork0.21205 ---
obs0.21472 17330 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.63 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2--6.15 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 4 229 2104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0221942
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.9832625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79125.60491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07215408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4281512
X-RAY DIFFRACTIONr_chiral_restr0.1490.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021406
X-RAY DIFFRACTIONr_nbd_refined0.2640.21107
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21385
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2183
X-RAY DIFFRACTIONr_metal_ion_refined0.1830.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.215
X-RAY DIFFRACTIONr_mcbond_it1.6591.51220
X-RAY DIFFRACTIONr_mcangle_it2.55821887
X-RAY DIFFRACTIONr_scbond_it4.8393866
X-RAY DIFFRACTIONr_scangle_it6.8834.5733
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 66 -
Rwork0.318 1222 -
obs--98.85 %

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