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- PDB-4i9f: Crystal structure of glycerol phosphate phosphatase Rv1692 from M... -

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Basic information

Entry
Database: PDB / ID: 4i9f
TitleCrystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium tuberculosis in complex with calcium
ComponentsGlycerol 3-phosphate phosphatase
KeywordsHYDROLASE / Haloacid dehalogenase superfamily / phosphatase / glycerol 3-phosphate binding
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 / metal ion binding
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
GCN5-related N-acetyltransferase-like domain-containing protein / D-glycerol 3-phosphate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_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

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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)76,3166
Polymers76,1602
Non-polymers1564
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-57 kcal/mol
Surface area30270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.814, 70.318, 97.099
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

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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, UniProt: L7N4Y2*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES (50 mM) pH 7.5 PEG 4000 (10% w/v), Sodium citrate trihydrate (40 mM), and CaCl2 (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: 2.2→50 Å / Num. all: 31079 / Num. obs: 30613 / % possible obs: 98.5 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PDW

3pdw


Resolution: 2.21→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.084 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24284 1640 5.1 %RANDOM
Rwork0.19102 ---
obs0.19373 30613 97.27 %-
all-31079 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.093 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å2-0.26 Å2
2--0 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.21→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 0 4 331 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195081
X-RAY DIFFRACTIONr_bond_other_d0.0010.024919
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.966919
X-RAY DIFFRACTIONr_angle_other_deg0.765311233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67623.062209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58415776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5031553
X-RAY DIFFRACTIONr_chiral_restr0.0610.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021125
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: 2.207→2.264 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 80 -
Rwork0.272 1665 -
obs--72.29 %

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