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- PDB-4i9g: Crystal structure of glycerol phosphate phosphatase Rv1692 from M... -

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Basic information

Entry
Database: PDB / ID: 4i9g
TitleCrystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium tuberculosis in complex with magnesium
ComponentsGlycerol 3-phosphate phosphatase
KeywordsHYDROLASE / Haloacid dehalogenaze superfamily / glycerol 3-phosphate phosphatase
Function / homology
Function and homology information


glycerol-1-phosphatase activity / glycerophospholipid catabolic process / glycerol metabolic process / cobalt ion binding / phosphatase activity / manganese ion binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #290 / GCN5-related N-acetyltransferase-like domain / GCN5-related N-acetyltransferase like domain / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / GMP Synthetase; Chain A, domain 3 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...GMP Synthetase; Chain A, domain 3 - #290 / GCN5-related N-acetyltransferase-like domain / GCN5-related N-acetyltransferase like domain / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / GMP Synthetase; Chain A, domain 3 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-glycerol 3-phosphate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsBiswas, T. / Larrouy-Maumus, G. / de Carvalho, L.P. / Tsodikov, O.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in Mycobacterium tuberculosis.
Authors: Larrouy-Maumus, G. / Biswas, T. / Hunt, D.M. / Kelly, G. / Tsodikov, O.V. / de Carvalho, L.P.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Glycerol 3-phosphate phosphatase
B: Glycerol 3-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2094
Polymers76,1602
Non-polymers492
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-38 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.368, 71.196, 94.621
Angle α, β, γ (deg.)90.00, 105.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycerol 3-phosphate phosphatase


Mass: 38079.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1731, Rv1692 / Production host: Escherichia coli (E. coli) / References: UniProt: O33194
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl (100 mM) pH 8.0, PEG 4000 (15% w/v), and MgCl2 (100 mM), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 12323 / Num. obs: 11153 / % possible obs: 90.5 % / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→40 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 26.539 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27237 556 4.7 %RANDOM
Rwork0.21979 ---
obs0.22225 11153 99.78 %-
all-12323 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.901 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å22.87 Å2
2---1.57 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 3.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 2 2 4787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194863
X-RAY DIFFRACTIONr_bond_other_d0.0050.024722
X-RAY DIFFRACTIONr_angle_refined_deg0.9331.9616619
X-RAY DIFFRACTIONr_angle_other_deg0.714310779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0965649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47223.163196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28715737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3371549
X-RAY DIFFRACTIONr_chiral_restr0.0490.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021069
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 36 -
Rwork0.312 798 -
obs--99.76 %

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