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- PDB-2pqv: Crystal structure of MutT/nudix family protein from Streptococcus... -

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Basic information

Entry
Database: PDB / ID: 2pqv
TitleCrystal structure of MutT/nudix family protein from Streptococcus pneumoniae
ComponentsMutT/nudix family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MutT/nudix family protein / Streptococcus pneumoniae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / MutT/nudix family protein / MutT/nudix family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsChang, C. / Binkowski, T.A. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of MutT/nudix family protein from Streptococcus pneumoniae.
Authors: Chang, C. / Binkowski, T.A. / Zhou, M. / Abdullah, J. / Joachimiak, A.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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: MutT/nudix family protein
B: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5683
Polymers35,4732
Non-polymers951
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-20 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.321, 64.675, 49.449
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MutT/nudix family protein


Mass: 17736.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0119 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q97T37, UniProt: A0A0H2UMZ7*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 20% PEG3350, 0.2 M Ammonium chloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 37031 / Num. obs: 36665 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 19.772 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.68
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.85 / Num. unique all: 3365 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.63→47.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.339 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22646 1833 5 %RANDOM
Rwork0.16695 ---
all0.16993 34812 --
obs0.16993 34812 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.06 Å2
2--0.38 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.63→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 5 414 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222537
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9513452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1235315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77625.672134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14815456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7051512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021932
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21133
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21708
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1131.51587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65422490
X-RAY DIFFRACTIONr_scbond_it2.81531071
X-RAY DIFFRACTIONr_scangle_it3.9634.5956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 128 -
Rwork0.201 2414 -
obs--95.42 %
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)
11.0155-0.2736-0.02560.8588-0.01751.80360.00240.0429-0.19630.00120.0092-0.09180.08930.1161-0.0116-0.04070.00440.02-0.0397-0.0029-0.03145.41424.5458.137
22.3857-0.38140.36372.20580.45261.43630.05840.331-0.0287-0.02530.025-0.15510.03360.2797-0.0833-0.0407-0.02430.01680.0719-0.0074-0.082714.40929.53-2.168
30.9762-0.1814-0.35910.79330.01990.1371-0.0109-0.13210.03280.09520.02760.0068-0.1229-0.0584-0.0167-0.01590.00750.0074-0.0227-0.0047-0.0568-6.5634.65817.291
41.6426-1.48710.01213.3629-0.63910.5943-0.1727-0.3927-0.02840.33770.21710.1521-0.1074-0.1552-0.0443-0.02680.02430.01860.0820.0238-0.0222-19.65929.34822.639
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 204 - 23
2X-RAY DIFFRACTION1AA43 - 5146 - 54
3X-RAY DIFFRACTION1AA72 - 9475 - 97
4X-RAY DIFFRACTION1AA122 - 150125 - 153
5X-RAY DIFFRACTION2AA21 - 4224 - 45
6X-RAY DIFFRACTION2AA52 - 7155 - 74
7X-RAY DIFFRACTION2AA95 - 12198 - 124
8X-RAY DIFFRACTION3BB1 - 204 - 23
9X-RAY DIFFRACTION3BB43 - 5146 - 54
10X-RAY DIFFRACTION3BB72 - 9475 - 97
11X-RAY DIFFRACTION3BB122 - 150125 - 153
12X-RAY DIFFRACTION4BB21 - 4224 - 45
13X-RAY DIFFRACTION4BB52 - 7155 - 74
14X-RAY DIFFRACTION4BB95 - 12198 - 124

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