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- PDB-3p96: Crystal structure of Phosphoserine phosphatase SerB from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 3p96
TitleCrystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium, native form
ComponentsPhosphoserine phosphatase SerB
KeywordsHYDROLASE / SSGCID / Phosphoserine phosphatase SerB / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / SAD / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J.Struct.Funct.Genom. / 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.
#1: Journal: Tuberculosis (Edinb) / Year: 2014
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoserine phosphatase SerB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9744
Polymers43,8521
Non-polymers1223
Water2,018112
1
A: Phosphoserine phosphatase SerB
hetero molecules

A: Phosphoserine phosphatase SerB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9488
Polymers87,7042
Non-polymers2446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area7040 Å2
ΔGint-74 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.530, 109.190, 134.320
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 SerB


Mass: 43852.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: serB, MAV_3907 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE UNIPROT SEQUENCE #A0QJI1 IS BEING UPDATED

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M MgCl2, 0.1 M MES, 20% PEG6000, protein at 27.45mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.05→36.97 Å / Num. all: 30644 / Num. obs: 29584 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 38.011 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.05-2.14.30.5543.782382232191585.8
2.1-2.160.473.8125902169100
2.16-2.220.4234.312617209899.5
2.22-2.290.19996540150172.6
2.29-2.370.2646.412165200699.9
2.37-2.450.2217.311729193199.9
2.45-2.540.1868.611359187399.9
2.54-2.650.15810.511067181599.7
2.65-2.760.14811.99676167898.4
2.76-2.90.10214.6101441680100
2.9-3.060.08117.69511156999.9
3.06-3.240.06321.98936148999.9
3.24-3.470.05426.47921140598.4
3.47-3.740.04830.56947129197.4
3.74-4.10.04333.76251118297.4
4.1-4.580.03439.46289110999.7
4.58-5.290.03342.2555098099.7
5.29-6.480.02839476084999.9
6.48-9.170.02244379167199.7
9.17-36.970.01845.4197437393.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→36.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.038 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1493 5.1 %RANDOM
Rwork0.229 ---
all0.231 30644 --
obs0.231 29505 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.015 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2---0.53 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.05→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 6 112 3008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222937
X-RAY DIFFRACTIONr_bond_other_d0.0010.021914
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9824004
X-RAY DIFFRACTIONr_angle_other_deg0.94834671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14922.92113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3115463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6131530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_mcbond_it0.7221.51964
X-RAY DIFFRACTIONr_mcbond_other0.1671.5812
X-RAY DIFFRACTIONr_mcangle_it1.30123145
X-RAY DIFFRACTIONr_scbond_it2.1313973
X-RAY DIFFRACTIONr_scangle_it3.3854.5858
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.537 97 -
Rwork0.558 1805 -
all-1902 -
obs-2232 85.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.94441.99070.20524.08290.25633.9361-0.1383-0.19610.23620.0874-0.08870.0625-0.55970.28290.2270.4543-0.1663-0.07280.1157-0.01760.077337.69465.55451.801
22.20241.00362.09994.03243.48515.1753-0.1097-0.32170.25120.42310.0289-0.18640.0080.34580.08080.5592-0.1882-0.09750.2998-0.02130.109541.88566.76559.187
31.29090.90820.02892.42360.42053.9299-0.023-0.0764-0.1707-0.0134-0.0794-0.19480.39160.09550.10230.3493-0.12060.03490.06670.01620.076133.23344.92942.296
41.23790.51161.45060.6411.0224.2617-0.1030.2683-0.1875-0.02210.1001-0.05730.56910.27880.00290.4403-0.14080.06380.1134-0.0330.146131.81738.51729.41
51.56321.66861.36323.23453.18384.24530.0382-0.04780.00450.0535-0.22680.22880.3853-0.40580.18870.5846-0.2799-0.02930.3246-0.03990.183414.98432.71611.054
66.66417.17286.889814.01463.5459.5081-0.98680.0060.9373-0.86110.17681.2728-1.1045-0.14990.810.7976-0.1994-0.18770.4338-0.09370.367115.27741.6094.924
70.77060.82310.78131.84412.18134.49180.01380.0756-0.0471-0.08290.0923-0.03050.2089-0.0384-0.10610.4721-0.2115-0.01590.2-0.02270.18624.8338.15215.241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 46
2X-RAY DIFFRACTION2A47 - 81
3X-RAY DIFFRACTION3A82 - 141
4X-RAY DIFFRACTION4A142 - 194
5X-RAY DIFFRACTION5A195 - 278
6X-RAY DIFFRACTION6A279 - 289
7X-RAY DIFFRACTION7A290 - 400

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