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

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Basic information

Entry
Database: PDB / ID: 5jma
TitleCrystal structure of Mycobacterium avium SerB2 in complex with serine at catalytic (PSP) 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: 2.03 Å
AuthorsShree, S. / Dubey, S. / Agrawal, A. / 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 catalytic (PSP) 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 28, 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)42,0415
Polymers41,7881
Non-polymers2544
Water1,946108
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,08310
Polymers83,5762
Non-polymers5078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6990 Å2
ΔGint-46 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.968, 109.645, 134.246
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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QJI1, phosphoserine phosphatase
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 25% PEG 8000, 0.1 M Magnesium acetate, 0.1 M HEPES pH 6.6, 0.1 - 0.5 M ortho phospho 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: 2.03→33.561 Å / Num. obs: 58573 / % possible obs: 99.3 % / Redundancy: 7.7 % / Net I/σ(I): 11.529
Reflection shellResolution: 2.03→2.1 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: 2.03→33.561 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.63
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2559 3806 6.5 %
Rwork0.2103 --
obs0.2132 58573 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.08 Å2 / Biso mean: 49.6018 Å2 / Biso min: 21.56 Å2
Refinement stepCycle: final / Resolution: 2.03→33.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 16 108 2978
Biso mean--58.98 55.66 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072901
X-RAY DIFFRACTIONf_angle_d0.9983955
X-RAY DIFFRACTIONf_chiral_restr0.04502
X-RAY DIFFRACTIONf_plane_restr0.004515
X-RAY DIFFRACTIONf_dihedral_angle_d12.4341010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0299-2.05560.38541290.37881898202791
2.0556-2.08260.43231380.36491951208998
2.0826-2.11110.37791390.34162029216899
2.1111-2.14130.37051390.30722035217499
2.1413-2.17320.33371330.29612007214099
2.1732-2.20720.28811460.28852056220299
2.2072-2.24340.31841400.27482027216799
2.2434-2.2820.31711460.2812005215199
2.282-2.32350.30951410.24412043218499
2.3235-2.36820.2861450.245320622207100
2.3682-2.41650.26711390.235719712110100
2.4165-2.46910.27441450.215520822227100
2.4691-2.52650.27521370.222320192156100
2.5265-2.58960.27751430.210220612204100
2.5896-2.65960.29031440.217420292173100
2.6596-2.73790.28631440.223120302174100
2.7379-2.82620.25521360.208320352171100
2.8262-2.92710.30061440.213420302174100
2.9271-3.04430.29031460.202720562202100
3.0443-3.18270.21781390.191620662205100
3.1827-3.35040.24741450.187120122157100
3.3504-3.56010.25391440.178820602204100
3.5601-3.83460.23831400.185320372177100
3.8346-4.21980.21031390.169120622201100
4.2198-4.82890.18451420.172220152157100
4.8289-6.0780.24361380.206220442182100
6.078-33.56610.22651450.191720452190100
Refinement TLS params.Method: refined / Origin x: -5.2245 Å / Origin y: -11.038 Å / Origin z: -38.7809 Å
111213212223313233
T0.3679 Å2-0.1228 Å20.0062 Å2-0.2976 Å2-0.0044 Å2--0.2747 Å2
L0.8463 °20.7225 °21.2151 °2-1.2866 °21.2496 °2--2.2366 °2
S-0.0738 Å °0.1528 Å °-0.0865 Å °-0.2407 Å °0.1341 Å °0.0042 Å °-0.0209 Å °0.19 Å °-0.0653 Å °
Refinement TLS groupSelection details: all

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