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- PDB-1l7m: HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (... -

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Basic information

Entry
Database: PDB / ID: 1l7m
TitleHIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (PI COMPLEX)
ComponentsPhosphoserine Phosphatase
KeywordsHYDROLASE / Rossmann Fold / four-Helix bundle / b-hairpin / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / dephosphorylation / magnesium ion binding / cytoplasm
Similarity search - Function
Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphoserine phosphatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWang, W. / Cho, H.S. / Kim, R. / Jancarik, J. / Yokota, H. / Nguyen, H.H. / Grigoriev, I.V. / Wemmer, D.E. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states.
Authors: Wang, W. / Cho, H.S. / Kim, R. / Jancarik, J. / Yokota, H. / Nguyen, H.H. / Grigoriev, I.V. / Wemmer, D.E. / Kim, S.H.
History
DepositionMar 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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 / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoserine Phosphatase
B: Phosphoserine Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9798
Polymers47,5512
Non-polymers4286
Water7,494416
1
A: Phosphoserine Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0855
Polymers23,7751
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoserine Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8953
Polymers23,7751
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.073, 70.270, 90.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphoserine Phosphatase / / PSP / O-phosphoserine phosphohydrolase / PSPase


Mass: 23775.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ1594 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3)/pSJS1244 / References: UniProt: Q58989, phosphoserine phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.68 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG 200 MME, 0.2M SODIUM PHOSPHATE, 0.1M ACETATE BUFFER, 5mM MgCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
pH: 7.5 / Details: Wang, W., (2001) Struct. Fold. Des., 9, 65.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
20.3 M1dropNaCl
31 mMEDTA1drop
410 mMdithiothreitol1drop
554 mg/mlprotein1drop
60.1 Msodium acetate1reservoir
70.5 Msodium phosphate dihydrate1reservoir
822 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000
RadiationMonochromator: ALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 70604 / Num. obs: 70604 / % possible obs: 0.989 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 36
Reflection shellResolution: 1.48→1.5 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 3547 / Rsym value: 0.335 / % possible all: 0.974
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 72554 / % possible obs: 98.9 % / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 97.4 % / Num. unique obs: 3547 / Rmerge(I) obs: 0.335

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F5S

1f5s


Resolution: 1.48→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 7366 10 %random
Rwork0.202 ---
all-70604 --
obs-63497 --
Displacement parametersBiso mean: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.451 Å20 Å2
3----0.201 Å2
Refinement stepCycle: LAST / Resolution: 1.48→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 22 416 3812
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.62

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