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- PDB-5jjb: Crystal structure of Mycobacterium avium SerB2 mutant D343G -

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Basic information

Entry
Database: PDB / ID: 5jjb
TitleCrystal structure of Mycobacterium avium SerB2 mutant D343G
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
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: 2.305 Å
AuthorsShree, S. / Dubey, 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
DepositionApr 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 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)41,8163
Polymers41,7301
Non-polymers862
Water1,982110
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6326
Polymers83,4602
Non-polymers1734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6710 Å2
ΔGint-47 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.101, 109.507, 133.319
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: 41729.785 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: D343G,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) / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 22-23% 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: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→36.88 Å / Num. obs: 20917 / % possible obs: 96.2 % / Redundancy: 7.7 % / Net I/σ(I): 18.3
Reflection shellResolution: 2.31→2.35 Å

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Processing

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

3p96


Resolution: 2.305→36.88 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.18
RfactorNum. reflection% reflection
Rfree0.2419 1998 9.55 %
Rwork0.1869 --
obs0.1924 20917 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.88 Å2 / Biso mean: 48.7134 Å2 / Biso min: 26.72 Å2
Refinement stepCycle: final / Resolution: 2.305→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 5 110 2996
Biso mean--65.96 49.51 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072918
X-RAY DIFFRACTIONf_angle_d1.0263974
X-RAY DIFFRACTIONf_chiral_restr0.038500
X-RAY DIFFRACTIONf_plane_restr0.004519
X-RAY DIFFRACTIONf_dihedral_angle_d11.8811049
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 (%)
2.3053-2.36290.30971150.27351086120178
2.3629-2.42680.30581230.23381156127984
2.4268-2.49820.28181300.22841236136689
2.4982-2.57880.30611390.22181315145495
2.5788-2.67090.31781450.22731368151399
2.6709-2.77790.28991460.23613891535100
2.7779-2.90420.29421470.207714011548100
2.9042-3.05730.25871480.208413951543100
3.0573-3.24870.23831470.206313851532100
3.2487-3.49940.25481480.186114001548100
3.4994-3.85120.23051500.161114221572100
3.8512-4.40770.20691510.152214361587100
4.4077-5.55020.19691510.16114201571100
5.5502-36.88460.22011580.17915101668100
Refinement TLS params.Method: refined / Origin x: -5.1826 Å / Origin y: -11.0475 Å / Origin z: -38.7653 Å
111213212223313233
T0.3557 Å2-0.1878 Å20.0022 Å2-0.3669 Å20.0052 Å2--0.3248 Å2
L0.6978 °20.5448 °20.8699 °2-1.2442 °21.1861 °2--2.6715 °2
S0.0313 Å °0.0181 Å °-0.0657 Å °0.0389 Å °-0.0258 Å °0.013 Å °0.2383 Å °0.0054 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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