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- PDB-5jlr: Crystal structure of Mycobacterium avium SerB2 with serine presen... -

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Basic information

Entry
Database: PDB / ID: 5jlr
TitleCrystal structure of Mycobacterium avium SerB2 with serine present at slightly different position near 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: 2.261 Å
AuthorsShree, S. / Agrawal, A. / Dubey, S. / Ramachandran, R.
Funding support India, 1items
OrganizationGrant numberCountry
CSIR India
Citation
Journal: To be published
Title: Crystal structure of Mycobacterium avium SerB2 with serine present at slightly different position near 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 ...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
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)42,0995
Polymers41,7881
Non-polymers3124
Water1,36976
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 area6830 Å2
ΔGint-48 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.498, 107.805, 133.743
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, 80 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#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.: 76 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
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: 2.26→24.195 Å / Num. obs: 22857 / % possible obs: 98.5 % / Redundancy: 7.2 % / Net I/σ(I): 21.52
Reflection shellResolution: 2.26→2.3 Å

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Processing

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

3p96


Resolution: 2.261→24.195 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.42
RfactorNum. reflection% reflection
Rfree0.2505 2000 8.75 %
Rwork0.1886 --
obs0.194 22857 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.22 Å2 / Biso mean: 56.6372 Å2 / Biso min: 29.21 Å2
Refinement stepCycle: final / Resolution: 2.261→24.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 20 76 2979
Biso mean--65.26 53.33 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072934
X-RAY DIFFRACTIONf_angle_d1.0323995
X-RAY DIFFRACTIONf_chiral_restr0.04502
X-RAY DIFFRACTIONf_plane_restr0.004522
X-RAY DIFFRACTIONf_dihedral_angle_d13.111035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2609-2.31740.31381340.24681394152893
2.3174-2.380.30791360.24961415155197
2.38-2.450.28121420.22511474161698
2.45-2.5290.27021380.22291450158898
2.529-2.61930.32561430.21121491163499
2.6193-2.7240.26281420.22021486162899
2.724-2.84780.31361430.21961483162699
2.8478-2.99770.28211430.20451494163799
2.9977-3.18510.28211440.20411514165899
3.1851-3.43040.22951440.19011490163499
3.4304-3.77450.25541440.18415051649100
3.7745-4.3180.20821460.162215241670100
4.318-5.430.19531470.15881536168399
5.43-24.19610.25631540.17421601175599
Refinement TLS params.Method: refined / Origin x: -5.4887 Å / Origin y: -10.6903 Å / Origin z: -38.6577 Å
111213212223313233
T0.4696 Å2-0.2335 Å20.0253 Å2-0.3589 Å2-0.027 Å2--0.3505 Å2
L0.9617 °20.6394 °21.2746 °2-1.3894 °21.3851 °2--4.1719 °2
S-0.0794 Å °0.0998 Å °-0.1176 Å °-0.0949 Å °0.0561 Å °0.0115 Å °0.2851 Å °0.0003 Å °0.0113 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 400
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allD1
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allS1 - 87
6X-RAY DIFFRACTION1allB1

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