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- PDB-5it0: Crystal structure of Mycobacterium avium SerB2 mutant D343N/D347N -

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Basic information

Entry
Database: PDB / ID: 5it0
TitleCrystal structure of Mycobacterium avium SerB2 mutant D343N/D347N
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / HAD family / phosphoserine phosphatase / catalytic site mutant
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: 1.968 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) active site mutant D343N/D347N
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 16, 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)41,8102
Polymers41,7861
Non-polymers241
Water1,928107
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6204
Polymers83,5722
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6200 Å2
ΔGint-57 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.945, 109.472, 133.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

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Components

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


Mass: 41785.852 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R, D343N, D347N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 57.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 22- 25% PEG 8000, 0.1 M Magnesium acetate tetrahydrate, 0.1 M HEPES pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.968→50 Å / Num. obs: 34256 / % possible obs: 98.8 % / Redundancy: 6.1 % / Net I/σ(I): 16.24
Reflection shellResolution: 1.98→2.05 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: 1.968→40.17 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 33.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1989 5.81 %
Rwork0.2099 32266 -
obs0.2132 34255 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.05 Å2 / Biso mean: 57.1017 Å2 / Biso min: 30.72 Å2
Refinement stepCycle: final / Resolution: 1.968→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 1 107 2990
Biso mean--46.27 56.42 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072917
X-RAY DIFFRACTIONf_angle_d1.0173976
X-RAY DIFFRACTIONf_chiral_restr0.039501
X-RAY DIFFRACTIONf_plane_restr0.004519
X-RAY DIFFRACTIONf_dihedral_angle_d11.8711050
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 (%)
1.9682-2.01740.38041280.3552074220291
2.0174-2.0720.40911370.39822226236397
2.072-2.13290.40081420.348422952437100
2.1329-2.20180.39061430.270123092452100
2.2018-2.28050.43721380.31792221235997
2.2805-2.37180.29821440.234723222466100
2.3718-2.47970.27971400.217423022442100
2.4797-2.61040.28071430.219323132456100
2.6104-2.77390.28851430.229923232466100
2.7739-2.9880.31891440.231223532497100
2.988-3.28860.29221440.215623352479100
3.2886-3.76420.26951450.197223412486100
3.7642-4.74120.19711460.160623802526100
4.7412-40.17870.21631520.17632472262499
Refinement TLS params.Method: refined / Origin x: -5.0388 Å / Origin y: -11.0336 Å / Origin z: -38.8786 Å
111213212223313233
T0.497 Å2-0.1741 Å2-0.0012 Å2-0.3508 Å2-0.0018 Å2--0.3501 Å2
L1.027 °20.5947 °20.8736 °2-1.1268 °21.0722 °2--3.178 °2
S0.0457 Å °0.0309 Å °-0.102 Å °0.008 Å °-0.0484 Å °0.0103 Å °0.3398 Å °-0.0767 Å °0.0009 Å °
Refinement TLS groupSelection details: all

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