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- PDB-1vmg: Crystal structure of MazG nucleotide pyrophosphohydrolase (138166... -

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Basic information

Entry
Database: PDB / ID: 1vmg
TitleCrystal structure of MazG nucleotide pyrophosphohydrolase (13816655) from Sulfolobus solfataricus at 1.46 A resolution
ComponentsHypothetical protein SSO3215Hypothesis
KeywordsHYDROLASE / 13816655 / MazG nucleotide pyrophosphohydrolase / Structural Genomics / JCSG / Protein Structure Initiative / PSI / Joint Center for Structural Genomics
Function / homologyNTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / : / Unknown ligand / MazG domain-containing protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of MazG nucleotide pyrophosphohydrolase (13816655) from Sulfolobus solfataricus at 1.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein SSO3215
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1893
Polymers11,1821
Non-polymers72
Water1,910106
1
A: Hypothetical protein SSO3215
hetero molecules

A: Hypothetical protein SSO3215
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3786
Polymers22,3642
Non-polymers144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area5530 Å2
ΔGint-47 kcal/mol
Surface area7710 Å2
MethodPISA
2
A: Hypothetical protein SSO3215
hetero molecules

A: Hypothetical protein SSO3215
hetero molecules

A: Hypothetical protein SSO3215
hetero molecules

A: Hypothetical protein SSO3215
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,75712
Polymers44,7294
Non-polymers288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_755-x+2,-y,z1
crystal symmetry operation15_645y+1,x-1,-z1
Buried area13600 Å2
ΔGint-126 kcal/mol
Surface area12880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.749, 79.749, 95.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-92-

HOH

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Components

#1: Protein Hypothetical protein SSO3215 / Hypothesis


Mass: 11182.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97U11, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.3 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 1.5M Li2SO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979834 / Wavelength: 0.979834,0.979694,1.020035
DetectorType: ADSC / Detector: CCD / Date: Sep 18, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9798341
20.9796941
31.0200351
ReflectionResolution: 1.46→25.62 Å / Num. obs: 25360 / % possible obs: 93.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 23.08 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.6
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2241 / Rsym value: 0.435 / % possible all: 57.6

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA4.2)data scaling
SHELXmodel building
autoSHARPphasing
REFMAC(5.2.0005)refinement
XDSdata reduction
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.46→25.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.453 / SU ML: 0.027 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. AN UNKNOWN ENTITY BETWEEN TYR 16 AND TRP 61 WAS AS UNK, UNKNOWN LIGAND. THE DENSITY LOOKS SIMILAR TO A GUANINE BASE. 3. THERE ARE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. AN UNKNOWN ENTITY BETWEEN TYR 16 AND TRP 61 WAS AS UNK, UNKNOWN LIGAND. THE DENSITY LOOKS SIMILAR TO A GUANINE BASE. 3. THERE ARE ADDITIONAL UNEXPLAINED DENSITIES NEAR ARG 23, TRP 31, TRP 61. IT MAY BE RELATED TO UNK, HOWEVER, DENSITY IS TOO FRAGMENTED TO IDENTIFY OR MODEL. 4. A LI ION WAS TENATIVELY MODELLED ACCORDING TO THE ENVIROMENT. AND ITS PRESENCE IN THE CRYSTALLIZATION BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.14633 1288 5.1 %RANDOM
Rwork0.14178 ---
obs0.14201 24059 93.34 %-
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: 14.062 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.46→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms655 0 10 106 771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022715
X-RAY DIFFRACTIONr_bond_other_d0.0010.02695
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.988971
X-RAY DIFFRACTIONr_angle_other_deg0.831625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.933582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01427.27333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.745151
X-RAY DIFFRACTIONr_chiral_restr0.0760.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02118
X-RAY DIFFRACTIONr_nbd_refined0.2530.2171
X-RAY DIFFRACTIONr_nbd_other0.1490.2624
X-RAY DIFFRACTIONr_nbtor_other0.0840.2387
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3810.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1330.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.225
X-RAY DIFFRACTIONr_mcbond_it1.9033444
X-RAY DIFFRACTIONr_mcbond_other0.3183171
X-RAY DIFFRACTIONr_mcangle_it2.3715708
X-RAY DIFFRACTIONr_scbond_it4.2798320
X-RAY DIFFRACTIONr_scangle_it5.36711263
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2360
X-RAY DIFFRACTIONr_metal_ion_refined0.2040.23
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 37 5.34 %
Rwork0.256 656 -
obs--35.07 %
Refinement TLS params.Method: refined / Origin x: 68.539 Å / Origin y: 7.845 Å / Origin z: 3.915 Å
111213212223313233
T-0.0081 Å20.0004 Å2-0.0002 Å2--0.0199 Å2-0.0041 Å2---0.0211 Å2
L0.4738 °2-0.2119 °20.08 °2-0.7849 °20.3208 °2--0.5075 °2
S0.0045 Å °0.003 Å °-0.0257 Å °0.0682 Å °-0.0261 Å °0.0546 Å °-0.0086 Å °-0.0386 Å °0.0216 Å °
Refinement TLS groupSelection: ALL

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