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- PDB-5is2: Crystal structure of Mycobacterium avium SerB2 at pH 6.6 -

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Basic information

Entry
Database: PDB / ID: 5is2
TitleCrystal structure of Mycobacterium avium SerB2 at pH 6.6
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
Phosphoserine phosphatase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å
AuthorsShree, S. / Ramachandran, R.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research (CSIR) India
Citation
Journal: To be published
Title: Crystal Structure of Mycobacterium avium SerB2 (MAV_3907) at pH 6.6
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
DepositionMar 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 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_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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)41,8122
Polymers41,7881
Non-polymers241
Water2,216123
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6244
Polymers83,5762
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6160 Å2
ΔGint-54 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.476, 109.494, 133.412
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: 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 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0QJI1, phosphoserine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Description: Mycobacterium avium SerB2 protein was crystallized in presence of its inhibitor rosaniline (a pink color compound) and pink coloured crystals were diffracted, however no density of ...Description: Mycobacterium avium SerB2 protein was crystallized in presence of its inhibitor rosaniline (a pink color compound) and pink coloured crystals were diffracted, however no density of rosaniline was found on solving the crystal data.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 22% PEG 8000, 0.1M 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 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 38932 / % possible obs: 98.4 % / Redundancy: 7.8 % / Net I/σ(I): 29

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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: 1.881→26.139 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1999 5.13 %
Rwork0.2033 36933 -
obs0.2048 38932 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.75 Å2 / Biso mean: 53.9969 Å2 / Biso min: 28.59 Å2
Refinement stepCycle: final / Resolution: 1.881→26.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 1 123 2959
Biso mean--43.89 55.91 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062868
X-RAY DIFFRACTIONf_angle_d0.9593915
X-RAY DIFFRACTIONf_chiral_restr0.037500
X-RAY DIFFRACTIONf_plane_restr0.004510
X-RAY DIFFRACTIONf_dihedral_angle_d12.031011
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 (%)
1.8807-1.92770.40771200.36442208232883
1.9277-1.97980.33241380.30082521265995
1.9798-2.03810.2881380.26762564270296
2.0381-2.10380.2861410.25812616275797
2.1038-2.1790.2511400.23592586272698
2.179-2.26620.25661440.2272656280099
2.2662-2.36920.28451470.217226992846100
2.3692-2.49410.27561440.209726572801100
2.4941-2.65020.27731440.213126942838100
2.6502-2.85460.28561460.233326892835100
2.8546-3.14140.23611470.226727212868100
3.1414-3.5950.22931470.193927202867100
3.595-4.52550.17811490.168327592908100
4.5255-26.1420.19941540.1782843299799
Refinement TLS params.Method: refined / Origin x: -4.9413 Å / Origin y: -10.7168 Å / Origin z: -38.6808 Å
111213212223313233
T0.4473 Å2-0.1857 Å20.0037 Å2-0.3306 Å2-0.0121 Å2--0.3173 Å2
L1.0084 °20.63 °20.8158 °2-1.3839 °20.9543 °2--2.9675 °2
S0.059 Å °0.0149 Å °-0.1369 Å °-0.0152 Å °-0.0456 Å °-0.0345 Å °0.3009 Å °-0.0517 Å °-0.0192 Å °
Refinement TLS groupSelection details: all

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