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- PDB-5vug: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase ... -

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Basic information

Entry
Database: PDB / ID: 5vug
TitleCrystal Structure of Glycerophosphoryl Diester Phosphodiesterase Domain of Uncharacterized Protein Rv2277c from Mycobacterium tuberculosis
ComponentsUncharacterized protein Rv2277c
KeywordsStructural genomics / Unknown function / alpha-beta fold / TIM barrel / glycerophosphodiester phosphodiesterase domain / MCSG / PSI-Biology / Midwest Center for Structural Genomics
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / Uncharacterized protein Rv2277c
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKim, Y. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: To Be Published
Title: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase Domain of Uncharacterized Protein Rv2277c from Mycobacterium tuberculosis
Authors: Kim, Y. / Li, H. / Endres, M. / Joachimiak, A.
History
DepositionMay 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 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 / 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.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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Rv2277c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6623
Polymers30,5301
Non-polymers1322
Water5,477304
1
A: Uncharacterized protein Rv2277c
hetero molecules

A: Uncharacterized protein Rv2277c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3256
Polymers61,0602
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3180 Å2
ΔGint-20 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.269, 43.878, 68.611
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
11A-430-

HOH

21A-506-

HOH

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Components

#1: Protein Uncharacterized protein Rv2277c


Mass: 30530.209 Da / Num. of mol.: 1 / Fragment: residues 24-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2277c, MTCY339.33 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) gold / References: UniProt: P9WLF1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Calcium Acetate, 0.1 M Imidazole:HCl pH 8.0, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 55320 / % possible obs: 98.3 % / Redundancy: 6.3 % / Rsym value: 0.094 / Net I/σ(I): 16.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1974 / CC1/2: 0.69 / Rsym value: 0.61 / % possible all: 71.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→26.275 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.45
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 2414 4.96 %random
Rwork0.1629 ---
obs0.1645 48689 87.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 7 304 2345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062092
X-RAY DIFFRACTIONf_angle_d0.8382858
X-RAY DIFFRACTIONf_dihedral_angle_d20.384752
X-RAY DIFFRACTIONf_chiral_restr0.078328
X-RAY DIFFRACTIONf_plane_restr0.006380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4968-1.52730.2133350.1783582X-RAY DIFFRACTION19
1.5273-1.56050.169640.18181156X-RAY DIFFRACTION38
1.5605-1.59680.23181050.17852017X-RAY DIFFRACTION66
1.5968-1.63670.22791420.17642604X-RAY DIFFRACTION85
1.6367-1.6810.24931660.16872834X-RAY DIFFRACTION93
1.681-1.73040.23761670.16442981X-RAY DIFFRACTION98
1.7304-1.78630.19121570.15793026X-RAY DIFFRACTION99
1.7863-1.85010.19131420.15743090X-RAY DIFFRACTION99
1.8501-1.92420.21861590.16113049X-RAY DIFFRACTION99
1.9242-2.01170.1851700.15463044X-RAY DIFFRACTION100
2.0117-2.11770.17671490.15053078X-RAY DIFFRACTION99
2.1177-2.25040.17231770.14633043X-RAY DIFFRACTION99
2.2504-2.4240.18311470.15073108X-RAY DIFFRACTION99
2.424-2.66770.18571450.16583115X-RAY DIFFRACTION99
2.6677-3.05320.21241580.16973133X-RAY DIFFRACTION100
3.0532-3.84480.19821570.17013171X-RAY DIFFRACTION99
3.8448-26.27930.18631740.16713244X-RAY DIFFRACTION97

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