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- PDB-4bx2: Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosp... -

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Basic information

Entry
Database: PDB / ID: 4bx2
TitleCrystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) in complex with Beryllium trifluoride
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 / regulation of mitotic nuclear division / cellular response to ATP / dephosphorylation ...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 / regulation of mitotic nuclear division / cellular response to ATP / dephosphorylation / myosin phosphatase activity / protein-serine/threonine phosphatase / growth factor binding / cleavage furrow / lamellipodium membrane / phosphoprotein phosphatase activity / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / actin cytoskeleton / midbody / postsynapse / glutamatergic synapse / 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
BERYLLIUM TRIFLUORIDE ION / Chronophin
Similarity search - Component
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 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)63,6879
Polymers63,2302
Non-polymers4577
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-29.8 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.830, 166.830, 166.830
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: (-0.1687, -0.9544, -0.2461), (-0.9503, 0.09123, 0.2975), (-0.2615, 0.2841, -0.9224)
Vector: 312.6, 246.7, 96.19)

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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-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.02 Å3/Da / Density % sol: 59.34 % / 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→44.59 Å / Num. obs: 39582 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.8 / % 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 2OYC

2oyc


Resolution: 2.193→44.587 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 1989 5 %
Rwork0.1678 --
obs0.1702 39580 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 45.53 Å2
Baniso -1Baniso -2Baniso -3
1--4.3006 Å2-0.102 Å20.7356 Å2
2--0.1215 Å20.6298 Å2
3----0.2862 Å2
Refinement stepCycle: LAST / Resolution: 2.193→44.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 28 188 4619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144569
X-RAY DIFFRACTIONf_angle_d1.5676192
X-RAY DIFFRACTIONf_dihedral_angle_d15.3091718
X-RAY DIFFRACTIONf_chiral_restr0.081689
X-RAY DIFFRACTIONf_plane_restr0.01832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1932-2.24810.36041520.2792685X-RAY DIFFRACTION100
2.2481-2.30890.30551390.2452637X-RAY DIFFRACTION100
2.3089-2.37680.26611290.22272678X-RAY DIFFRACTION100
2.3768-2.45350.23981370.20082685X-RAY DIFFRACTION100
2.4535-2.54120.26171390.19192666X-RAY DIFFRACTION100
2.5412-2.64290.2131400.17942660X-RAY DIFFRACTION100
2.6429-2.76320.26911380.17932677X-RAY DIFFRACTION100
2.7632-2.90880.22891370.17862669X-RAY DIFFRACTION100
2.9088-3.09110.20881510.16862661X-RAY DIFFRACTION100
3.0911-3.32960.20961410.15882677X-RAY DIFFRACTION100
3.3296-3.66460.20121460.15022673X-RAY DIFFRACTION100
3.6646-4.19450.16191390.14032725X-RAY DIFFRACTION100
4.1945-5.28330.18771370.13852718X-RAY DIFFRACTION100
5.2833-44.59640.20841640.1792780X-RAY DIFFRACTION100
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)
11.7792-0.2558-1.03243.25960.35791.6022-0.0268-0.35660.37310.6439-0.05190.3429-0.4882-0.4994-0.36440.55660.04910.05870.459-0.0420.3538127.0476119.034273.2641
23.4285-2.17760.56392.2975-0.97695.9818-0.1351-0.3667-0.76740.8428-0.0997-0.090.36130.4349-0.16750.3979-0.0199-0.01810.26750.00110.4018139.1814106.409269.5509
31.92520.2586-0.43591.1094-0.33551.3677-0.23970.3026-0.48260.03860.00480.0040.3888-0.2664-0.0540.2642-0.08340.03380.2838-0.11220.3968136.6232106.995954.2086
45.47640.75113.00861.03150.26271.6764-0.00691.2795-0.3907-0.50640.1120.0687-0.0473-1.00420.53560.40240.0143-0.04371.101-0.15850.3918141.4575111.851733.0336
51.83140.6067-1.08734.64170.39282.3903-0.11970.8372-0.6212-0.351-0.2460.01250.3718-0.3035-0.18980.2805-0.05410.0150.4865-0.14880.4391147.242109.846339.562
63.00481.5164-1.76881.3482-1.51412.33530.07350.332-0.1491-0.0101-0.1455-0.01180.0865-0.1795-0.06660.24410.0085-0.05910.2905-0.0230.3128146.3526121.18246.8176
72.2903-0.8281-1.15782.6484-0.90842.7853-0.0224-0.14850.05530.4287-0.0757-0.074-0.5085-0.1304-0.090.38110.0131-0.05530.2327-0.05570.2654133.9455121.3267.1499
81.35520.4857-0.2172.63250.41574.54290.16150.5690.9638-0.856-0.1440.1896-1.03620.20090.08130.6393-0.02020.03250.45730.29860.7978165.6935150.688529.0995
90.89670.63681.13015.96190.96272.8240.13640.2520.3766-0.638-0.035-0.9637-0.00790.5163-0.10080.2280.02990.08640.51730.20160.5928177.3305140.671532.0722
103.4292-0.35880.43184.61270.39791.8310.2825-0.45540.58180.7161-0.4071-0.4169-0.37420.65520.0580.2853-0.1911-0.09910.49610.03220.4816172.3703139.823853.5249
115.41461.75721.13872.53740.80870.39020.2759-0.4112-0.27460.3414-0.1606-0.30460.1840.2199-0.08040.2642-0.0891-0.08150.41990.11690.3816172.7605129.323852.4715
123.13471.088-0.57383.8086-1.40292.74010.22760.14140.7569-0.1687-0.23430.2219-0.4082-0.11890.09740.28020.0722-0.00010.26460.04930.5268158.4588142.306441.1819
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 291 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 1 THROUGH 64 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 65 THROUGH 81 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 82 THROUGH 115 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 116 THROUGH 151 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 152 THROUGH 290 )

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