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- PDB-5jlp: Crystal structure of Mycobacterium avium SerB2 in complex with se... -

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Basic information

Entry
Database: PDB / ID: 5jlp
TitleCrystal structure of Mycobacterium avium SerB2 in complex with serine at ACT domain
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / HAD family / phosphoserine phosphatase
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
: / ACT domain / ACT domain / haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / : / ACT domain / ACT domain profile. / ACT domain / ACT-like domain ...: / 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
SERINE / Phosphoserine phosphatase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsShree, S. / Ramachandran, R.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR India
Citation
Journal: To be published
Title: Crystal structure of Mycobacterium avium SerB2 in complex with serine at ACT domain
Authors: Shree, S. / Ramachandran, R.
#1: Journal: J. Struct. Funct. Genomics / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
History
DepositionApr 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0995
Polymers41,7881
Non-polymers3124
Water32418
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,19910
Polymers83,5762
Non-polymers6238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7060 Å2
ΔGint-47 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.548, 109.535, 134.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41787.820 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria)
Strain: 104 / Gene: serB, MAV_3907 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QJI1, phosphoserine phosphatase

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Non-polymers , 5 types, 22 molecules

#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-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 22% PEG 8000, 0.1 M Magnesium acetate tetrahydrate, 0.1M HEPES pH 6.6, 0.1 M L- Serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.495→35.24 Å / Num. obs: 29846 / % possible obs: 93.8 % / Redundancy: 2 % / Net I/σ(I): 8.65
Reflection shellResolution: 2.5→2.59 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P96

3p96


Resolution: 2.495→35.235 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.84
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2666 2983 9.99 %
Rwork0.1913 --
obs0.1991 29846 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.95 Å2 / Biso mean: 72.0464 Å2 / Biso min: 32.35 Å2
Refinement stepCycle: final / Resolution: 2.495→35.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 20 18 2849
Biso mean--65.63 60.47 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082861
X-RAY DIFFRACTIONf_angle_d1.1663906
X-RAY DIFFRACTIONf_chiral_restr0.047502
X-RAY DIFFRACTIONf_plane_restr0.005508
X-RAY DIFFRACTIONf_dihedral_angle_d13.36980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4951-2.5360.47511020.3059919102169
2.536-2.57970.33491300.29911165129583
2.5797-2.62660.39941380.27761193133189
2.6266-2.67710.38831400.29861252139292
2.6771-2.73170.42071420.28681323146593
2.7317-2.79110.36611480.281294144296
2.7911-2.8560.38641470.27011320146797
2.856-2.92740.37541540.26881334148897
2.9274-3.00650.34231510.2521325147697
3.0065-3.09490.47921480.24491356150497
3.0949-3.19480.26931490.22261327147697
3.1948-3.30890.26661490.20491308145796
3.3089-3.44120.22471410.19521321146296
3.4412-3.59770.30881500.1741314146496
3.5977-3.78720.25321470.18071320146796
3.7872-4.02410.19881510.16461313146495
4.0241-4.33430.21151320.1561305143795
4.3343-4.76960.21731420.15061291143395
4.7696-5.45750.20291470.16091315146294
5.4575-6.86760.29611340.18911278141294
6.8676-35.23870.21771410.15481290143192
Refinement TLS params.Method: refined / Origin x: -4.9071 Å / Origin y: -10.7477 Å / Origin z: -39.1907 Å
111213212223313233
T0.4323 Å2-0.1587 Å20.0606 Å2-0.4217 Å2-0.0206 Å2--0.4792 Å2
L0.6766 °20.2878 °20.6071 °2-0.9121 °20.6507 °2--4.4751 °2
S-0.0066 Å °0.0685 Å °-0.0402 Å °0.0386 Å °-0.1012 Å °0.0677 Å °0.6914 Å °-0.2453 Å °0.0787 Å °
Refinement TLS groupSelection details: all

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