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- PDB-5aes: Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosp... -

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Basic information

Entry
Database: PDB / ID: 5aes
TitleCrystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with a PNP-derived Inhibitor
ComponentsPYRIDOXAL PHOSPHATE PHOSPHATASE
KeywordsHYDROLASE / PDXP / PLPP / HALOACID DEHALOGENASE / HAD PHOSPHATASE / HAD 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 / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / growth factor binding / cleavage furrow / lamellipodium membrane / phosphoprotein phosphatase activity / dephosphorylation / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / actin cytoskeleton / midbody / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
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
Chem-5B0 / Chronophin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.751 Å
AuthorsKnobloch, G. / Jabari, N. / Koehn, M. / Gohla, A. / Schindelin, H.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Synthesis of Hydrolysis-Resistant Pyridoxal 5'-Phosphate Analogs and Their Biochemical and X-Ray Crystallographic Characterization with the Pyridoxal Phosphatase Chronophin.
Authors: Knobloch, G. / Jabari, N. / Stadlbauer, S. / Schindelin, H. / Kohn, M. / Gohla, A.
History
DepositionJan 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Atomic model / Other
Revision 1.2Jun 10, 2015Group: Database references
Revision 2.0Jun 28, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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 / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_source.type
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRIDOXAL PHOSPHATE PHOSPHATASE
B: PYRIDOXAL PHOSPHATE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8657
Polymers63,2302
Non-polymers6355
Water77543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-35.3 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.810, 166.810, 166.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1451, -0.2508, -0.9571), (-0.2571, -0.9246, 0.2812), (-0.9554, 0.2869, 0.06972)
Vector: 41.62, -100.3, 64.14)

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Components

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


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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-5B0 / {2-[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]ethyl}phosphonic acid


Mass: 247.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14NO5P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.04 Å3/Da / Density % sol: 59.54 % / Description: NONE
Crystal growpH: 8
Details: 0.1M IMIDAZOLE (PH 8.0), 0.2M NACL, 1M SODIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 2, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→32.71 Å / Num. obs: 20219 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 67.02 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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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 4BX3

4bx3


Resolution: 2.751→32.714 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1026 5.1 %
Rwork0.1895 --
obs0.1923 20098 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.3788 Å2-0.4678 Å2-1.0621 Å2
2--0.4361 Å20.3969 Å2
3---0.124 Å2
Refinement stepCycle: LAST / Resolution: 2.751→32.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 40 43 4486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064531
X-RAY DIFFRACTIONf_angle_d0.9326184
X-RAY DIFFRACTIONf_dihedral_angle_d14.1791685
X-RAY DIFFRACTIONf_chiral_restr0.044681
X-RAY DIFFRACTIONf_plane_restr0.004817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7505-2.89550.29621510.26132700X-RAY DIFFRACTION100
2.8955-3.07670.30251450.24342711X-RAY DIFFRACTION100
3.0767-3.31410.24811580.21322706X-RAY DIFFRACTION100
3.3141-3.64720.26461510.19662691X-RAY DIFFRACTION99
3.6472-4.1740.2911540.17572709X-RAY DIFFRACTION99
4.174-5.25530.18671250.16872734X-RAY DIFFRACTION99
5.2553-32.71640.23471420.18212821X-RAY DIFFRACTION99
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)
10.19950.1515-0.33010.4023-0.39250.6421-0.20820.0359-0.3249-0.1773-0.1754-0.18770.26690.1219-0.10250.22180.0085-0.00120.3699-0.10390.348540.1834-73.497948.2377
20.0049-0.0152-0.01740.03450.0270.0277-0.0502-0.12170.12620.1283-0.02070.38830.3048-0.1671-0.00010.265-0.03230.010.461-0.02560.300827.6961-69.84760.7523
30.17240.0182-0.09550.10160.15350.4639-0.0411-0.31650.28590.23090.2301-0.0940.17170.05170.38110.15-0.0217-0.09540.5019-0.18240.25229.9459-55.201660.5566
4-0.0001-0.00940.02630.044-0.06240.08840.067-0.09840.1326-0.05250.0943-0.09110.0691-0.1060.0480.2242-0.1134-0.07640.4534-0.27240.643125.7035-33.215855.2168
50.52670.23490.35260.43890.10120.2850.0421-0.41950.24610.2820.2604-0.1575-0.1457-0.07540.40610.1709-0.06650.00930.4743-0.14360.261419.8216-39.637157.0681
60.1777-0.0533-0.07460.0241-0.01680.15510.0272-0.07230.0264-0.06850.1657-0.1074-0.0701-0.05580.32380.1844-0.0818-0.01080.3903-0.03220.362620.8138-47.175245.8131
70.0303-0.08030.01240.16120.04690.4139-0.1507-0.0261-0.2703-0.18170.1407-0.08320.2953-0.0202-0.07220.2657-0.07110.01130.3452-0.11430.258433.0886-67.127645.5512
80.62550.118-0.66330.48880.01051.11930.33750.56910.2616-0.3289-0.02590.3463-0.6402-0.44480.27630.4265-0.0282-0.08140.57920.16350.326-1.9414-33.460819.1556
90.10220.0842-0.04720.0851-0.00760.0478-0.0463-0.0564-0.0363-0.0591-0.1150.00230.05530.0634-0.15090.216-0.546-0.2050.50140.11680.5635-5.7927-60.744633.0703
100.6516-0.13180.2380.2087-0.22740.51260.3306-0.13-0.4159-0.12930.03880.37390.189-0.08250.93540.1832-0.1337-0.10320.39440.07910.38912.4847-50.348835.0424
110.1778-0.2109-0.07040.48980.12760.06420.29740.26850.2048-0.43460.0607-0.0328-0.48150.25440.50040.4594-0.12830.14820.79230.12630.239810.2321-33.707816.0457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 25 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 26 THROUGH 49 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 50 THROUGH 100 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 101 THROUGH 115 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 116 THROUGH 151 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 152 THROUGH 219 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 220 THROUGH 290 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 100 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 101 THROUGH 115 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 116 THROUGH 219 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 220 THROUGH 291 )

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