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- PDB-1vp2: CRYSTAL STRUCTURE OF A PUTATIVE XANTHOSINE TRIPHOSPHATE PYROPHOSP... -

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Basic information

Entry
Database: PDB / ID: 1vp2
TitleCRYSTAL STRUCTURE OF A PUTATIVE XANTHOSINE TRIPHOSPHATE PYROPHOSPHATASE/HAM1 PROTEIN HOMOLOG (TM0159) FROM THERMOTOGA MARITIMA AT 1.78 A RESOLUTION
ComponentsPutative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
KeywordsHYDROLASE / PUTATIVE XANTHOSINE TRIPHOSPHATE PYROPHOSPHATASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


purine nucleoside triphosphate catabolic process / XTP/dITP diphosphatase / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding ...purine nucleoside triphosphate catabolic process / XTP/dITP diphosphatase / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
dITP/XTP pyrophosphatase / Ham1-like protein / Ham1 family / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
dITP/XTP pyrophosphatase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Xanthosine triphosphate pyrophosphatase1/HAM1 protein homolog (TM0159) from Thermotoga maritima at 1.78 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORT THE ASSIGNMENT OF THE TETRAMER AS THE BIOLOGICALLY SIGNIFICANT STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
B: Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0536
Polymers47,6692
Non-polymers3844
Water4,612256
1
A: Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
B: Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
hetero molecules

A: Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
B: Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,10712
Polymers95,3384
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)142.851, 142.851, 45.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative Xanthosine triphosphate pyrophosphatase/HAM1 protein homolog


Mass: 23834.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0159 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WY06, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.53 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 1.6M (NH4)2SO4, 0.1M NaCl, 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: 5.0.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Mar 3, 2004
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→34.65 Å / Num. obs: 37599 / % possible obs: 83.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.82 Å2 / Rsym value: 0.089 / Net I/σ(I): 12.6
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1359 / Rsym value: 0.502 / % possible all: 42.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V7R

1v7r


Resolution: 1.78→34.65 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.286 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20473 1893 5 %RANDOM
Rwork0.16579 ---
obs0.16777 35706 82.86 %-
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: 21.043 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.78→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 20 256 3234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223055
X-RAY DIFFRACTIONr_bond_other_d0.0010.022823
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9654123
X-RAY DIFFRACTIONr_angle_other_deg0.88936575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95723.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4115547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.981516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
X-RAY DIFFRACTIONr_nbd_refined0.2180.2558
X-RAY DIFFRACTIONr_nbd_other0.1840.22717
X-RAY DIFFRACTIONr_nbtor_other0.0850.21743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.215
X-RAY DIFFRACTIONr_mcbond_it2.48532060
X-RAY DIFFRACTIONr_mcbond_other0.6443768
X-RAY DIFFRACTIONr_mcangle_it3.0953049
X-RAY DIFFRACTIONr_scbond_it5.26481297
X-RAY DIFFRACTIONr_scangle_it7.232111074
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 79 5.81 %
Rwork0.211 1280 -
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)
11.3687-0.9743-0.16111.9763-0.00210.71280.0094-0.18950.06050.2085-0.0366-0.1283-0.0738-0.01030.0271-0.0758-0.0351-0.01150.0011-0.0018-0.083754.047731.97337.0013
22.194-0.87550.27181.4645-0.31711.04960.0840.2323-0.186-0.1634-0.04780.081-0.0145-0.0785-0.0362-0.02360.0245-0.0233-0.0828-0.0244-0.073331.912710.1906-7.496
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 3 - 191 / Label seq-ID: 15 - 203

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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