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- PDB-2oyc: Crystal structure of human pyridoxal phosphate phosphatase -

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Basic information

Entry
Database: PDB / ID: 2oyc
TitleCrystal structure of human pyridoxal phosphate phosphatase
ComponentsPyridoxal phosphate phosphatase
KeywordsHYDROLASE / Phosphatase / Structural Genomics / NYSGXRC / New York SGX Research Center for Structural Genomics / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / positive regulation of actin filament depolymerization / regulation of modification of postsynaptic structure / dephosphorylation / regulation of mitotic nuclear division / protein-serine/threonine phosphatase / cellular response to ATP ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / positive regulation of actin filament depolymerization / regulation of modification of postsynaptic structure / dephosphorylation / regulation of mitotic nuclear division / protein-serine/threonine phosphatase / cellular response to ATP / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / lamellipodium membrane / protein dephosphorylation / heat shock protein binding / regulation of cytokinesis / ruffle membrane / cell-cell junction / cytoskeleton / postsynapse / glutamatergic synapse / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
2-phosphoglycolate phosphatase, eukaryotic / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Chronophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRamagopal, U.A. / Freeman, J. / Izuka, M. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Struct.Funct.Genom. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 1.6Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4123
Polymers33,1411
Non-polymers2712
Water3,027168
1
A: Pyridoxal phosphate phosphatase
hetero molecules

A: Pyridoxal phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8246
Polymers66,2822
Non-polymers5424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)54.329, 54.329, 213.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

DetailsProbable dimer

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Components

#1: Protein Pyridoxal phosphate phosphatase / PLP phosphatase


Mass: 33140.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDXP, PLP, PLPP / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96GD0, pyridoxal phosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 40% PEG4000, 0.1M Sodium citrate pH 5.6, 20% Isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 35004 / Num. obs: 35004 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.058 / Χ2: 0.816 / Net I/σ(I): 26.4
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.16 / Num. unique all: 6442 / Rsym value: 0.633 / Χ2: 0.514 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZJJ

1zjj


Resolution: 1.72→26.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.36 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1755 5 %RANDOM
Rwork0.192 ---
all0.193 34933 --
obs0.193 34933 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.72→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 6 168 2507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212392
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9843259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1865319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66820.741108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71915383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7711538
X-RAY DIFFRACTIONr_chiral_restr0.1080.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021891
X-RAY DIFFRACTIONr_nbd_refined0.2250.21055
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.214
X-RAY DIFFRACTIONr_mcbond_it1.351.51533
X-RAY DIFFRACTIONr_mcangle_it2.31922446
X-RAY DIFFRACTIONr_scbond_it3.6593874
X-RAY DIFFRACTIONr_scangle_it5.9314.5813
LS refinement shellResolution: 1.72→1.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 111 -
Rwork0.26 2391 -
obs-2502 98.7 %

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