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- PDB-5t41: Crystal structure of Mycobacterium avium SerB2 mutant S275A/R279A... -

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Basic information

Entry
Database: PDB / ID: 5t41
TitleCrystal structure of Mycobacterium avium SerB2 mutant S275A/R279A at pH 6.6 with ethylene glycol bound at ACT- I domain
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / HAD family / phosphoserine phosphatase
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / dephosphorylation / magnesium ion binding
Similarity search - Function
: / ACT domain / ACT domain / haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / HAD superfamily/HAD-like ...: / ACT domain / ACT domain / haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoserine phosphatase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.149 Å
AuthorsShree, S. / Dubey, S. / Ramachandran, R.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR India
CitationJournal: To be published
Title: Crystal Structure of Mycobacterium avium SerB2 (MAV_3907) at pH 6.6
Authors: Shree, S. / Ramachandran, R.
History
DepositionAug 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7723
Polymers41,6861
Non-polymers862
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.817, 108.792, 132.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Phosphoserine phosphatase / PSPase / O-phosphoserine phosphohydrolase


Mass: 41685.703 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R, S275A, R279A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria)
Strain: 104 / Gene: serB, MAV_3907 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QJI1, phosphoserine phosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 24% PEG 8000, 0.2M Magnesium acetate tetrahydrate, 0.1M HEPES pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.15→41.999 Å / Num. obs: 15906 / % possible obs: 95.8 % / Redundancy: 3 % / Net I/σ(I): 6.01
Reflection shellResolution: 3.15→3.26 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P96

3p96


Resolution: 3.149→41.999 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2929 1583 9.95 %
Rwork0.2372 14322 -
obs0.2428 15905 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.83 Å2 / Biso mean: 62.5055 Å2 / Biso min: 27.79 Å2
Refinement stepCycle: final / Resolution: 3.149→41.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 5 42 2899
Biso mean--44.67 46.33 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012890
X-RAY DIFFRACTIONf_angle_d1.2163945
X-RAY DIFFRACTIONf_chiral_restr0.063500
X-RAY DIFFRACTIONf_plane_restr0.006516
X-RAY DIFFRACTIONf_dihedral_angle_d13.6991742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1485-3.25010.33111280.29331129125784
3.2501-3.36620.38331350.27881189132488
3.3662-3.5010.3581340.30151223135791
3.501-3.66020.31961440.27091297144194
3.6602-3.85310.34951470.25051332147998
3.8531-4.09430.32731500.25381341149199
4.0943-4.41010.25051500.224513671517100
4.4101-4.85330.24371460.202913681514100
4.8533-5.55420.30391440.218713481492100
5.5542-6.99250.2781520.286813681520100
6.9925-42.00250.25711530.189913601513100
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)
11.32071.26620.33743.6150.7212.72830.1663-0.206-0.05350.5-0.1409-0.06350.2490.1369-0.01550.7242-0.2617-0.05650.61130.0220.58323.8731-1.0971-19.1918
21.3717-0.07740.19591.29350.7571.3755-0.01360.0812-0.80060.64940.1903-0.09010.05970.03190.02410.6484-0.3842-0.04470.61180.04130.7438-0.9025-11.1459-40.4344
31.71461.98730.96622.26371.46893.9730.0730.081-0.05740.1207-0.08740.17810.5873-0.15710.03480.657-0.2584-0.01050.6435-0.04340.6976-13.6165-18.1422-53.0444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 165 )A5 - 165
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 186 )A166 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 400 )A187 - 400

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