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- PDB-1l7p: SUBSTRATE BOUND PHOSPHOSERINE PHOSPHATASE COMPLEX STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1l7p
TitleSUBSTRATE BOUND PHOSPHOSERINE PHOSPHATASE COMPLEX STRUCTURE
ComponentsPHOSPHOSERINE PHOSPHATASE
KeywordsHYDROLASE / Rossmann fold / beta-hairpin / four-helix bundle / 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 / Phosphoserine phosphatase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)48,1096
Polymers47,5492
Non-polymers5604
Water3,513195
1
A: PHOSPHOSERINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9592
Polymers23,7741
Non-polymers1851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOSERINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1494
Polymers23,7741
Non-polymers3753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.799, 70.428, 90.045
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: 23774.361 Da / Num. of mol.: 2 / Mutation: D11N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/pSJS1244 / References: UniProt: Q58989, phosphoserine phosphatase
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE / Phosphoserine


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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 % / Description: 1 degree oscillation
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 2K MME, SODIUM SULFATE, SODIUM ACTATE, PLS, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jan 28, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 35267 / Num. obs: 33257 / % possible obs: 0.943 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.928 Å2 / Rsym value: 0.049 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.98 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 1800 / Rsym value: 0.251 / % possible all: 0.933

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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: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 3357 10 %RANDOM
Rwork0.229 ---
all-33257 --
obs-32794 --
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 32 195 3505

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