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- PDB-4bx3: Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosp... -

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Basic information

Entry
Database: PDB / ID: 4bx3
TitleCrystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase)
ComponentsPYRIDOXAL PHOSPHATE PHOSPHATASE
KeywordsHYDROLASE / PDXP / HAD PHOSPHATASE / HAD-LIKE HYDROLASE
Function / homology
Function and homology information


pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / positive regulation of actin filament depolymerization / regulation of modification of postsynaptic structure / dephosphorylation / regulation of mitotic nuclear division / protein-serine/threonine phosphatase ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / 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 / cleavage furrow / phosphoprotein phosphatase activity / lamellipodium membrane / protein dephosphorylation / heat shock protein binding / regulation of cytokinesis / ruffle membrane / cell-cell junction / actin cytoskeleton / midbody / postsynapse / glutamatergic synapse / magnesium ion binding / protein homodimerization activity / 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
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsKnobloch, G. / Gohla, A. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Chronophin Dimerization is Required for Proper Positioning of its Substrate Specificity Loop.
Authors: Kestler, C. / Knobloch, G. / Tessmer, I. / Jeanclos, E. / Schindelin, H. / Gohla, A.
History
DepositionJul 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 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
B: PYRIDOXAL PHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4636
Polymers63,2302
Non-polymers2334
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-32.6 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.100, 167.100, 167.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-2076-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.08087, 0.9568, -0.2793), (0.9595, -0.1506, -0.2382), (-0.2699, -0.2488, -0.9302)
Vector: 63.05, -42.02, 100.3)

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Components

#1: Protein PYRIDOXAL PHOSPHATE PHOSPHATASE / PLP PHOSPHATASE / CHRONOPHIN / PLPP


Mass: 31614.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60487, pyridoxal phosphatase, phosphoserine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.04 Å3/Da / Density % sol: 59.53 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M IMIDAZOLE PH 8, 0.2M NACL, 1M SODIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.19→44.66 Å / Num. obs: 39743 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 47.02 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OYC

2oyc


Resolution: 2.193→44.659 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 1996 5 %
Rwork0.1707 --
obs0.1725 39741 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 48.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.6234 Å2-0.0039 Å20.0888 Å2
2---0.1768 Å20.6124 Å2
3---0.1106 Å2
Refinement stepCycle: LAST / Resolution: 2.193→44.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 14 178 4595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154550
X-RAY DIFFRACTIONf_angle_d1.646168
X-RAY DIFFRACTIONf_dihedral_angle_d15.911713
X-RAY DIFFRACTIONf_chiral_restr0.094688
X-RAY DIFFRACTIONf_plane_restr0.01829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.193-2.24780.27711460.23982622X-RAY DIFFRACTION99
2.2478-2.30860.25891420.23212694X-RAY DIFFRACTION100
2.3086-2.37650.26131360.21472696X-RAY DIFFRACTION100
2.3765-2.45320.22861320.20842688X-RAY DIFFRACTION100
2.4532-2.54090.25271410.2092683X-RAY DIFFRACTION100
2.5409-2.64260.28941390.19532661X-RAY DIFFRACTION100
2.6426-2.76290.24481380.20022679X-RAY DIFFRACTION100
2.7629-2.90850.25021410.19822701X-RAY DIFFRACTION100
2.9085-3.09070.24761510.18392678X-RAY DIFFRACTION100
3.0907-3.32930.2061420.16942690X-RAY DIFFRACTION100
3.3293-3.66420.20781480.16362698X-RAY DIFFRACTION100
3.6642-4.19410.17061390.14382722X-RAY DIFFRACTION100
4.1941-5.28270.17171350.13872734X-RAY DIFFRACTION100
5.2827-44.66860.18851660.17132799X-RAY DIFFRACTION100

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