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- PDB-5nm8: Structure of PipY, the COG0325 family member of Synechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 5nm8
TitleStructure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942, with PLP bound
ComponentsPipY
KeywordsPLP-binding protein / fold type III PLP-protein / vitamin B6 / pyridoxal phosphate / Schiff base
Function / homology
Function and homology information


pyridoxal phosphate binding
Similarity search - Function
Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Alanine racemase / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate homeostasis protein
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsTremino, L. / Forcada-Nadal, A. / Contreras, A. / Rubio, V.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish GovernmentBFU2014-58229-P Spain
Spanish GovernmentBES-2012-058304 Spain
Valencian GovernmentPrometeoII/2014/029 Spain
CitationJournal: FEBS Lett. / Year: 2017
Title: Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B6 -dependent epilepsy.
Authors: Tremino, L. / Forcada-Nadal, A. / Contreras, A. / Rubio, V.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Structure summary / Category: audit_author
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PipY
B: PipY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1345
Polymers50,6002
Non-polymers5343
Water2,918162
1
A: PipY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5472
Polymers25,3001
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PipY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5873
Polymers25,3001
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.627, 98.937, 103.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PipY


Mass: 25299.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria)
Gene: Synpcc7942_2060 / Plasmid: pET-22b(+)-2060 / Details (production host): a pET-22b+ derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31LH9
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.46 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes-Na pH 7.5 0.2 M Calcium acetate 18% (wt/vol) Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.93→71.6 Å / Num. obs: 37132 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Net I/σ(I): 22.3
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.051 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2409 / CC1/2: 0.87 / Rpim(I) all: 0.016 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB file 5NLC, chain A

5nlc


Resolution: 1.93→71.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.848 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23821 1754 4.7 %RANDOM
Rwork0.19485 ---
obs0.19694 35318 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å20 Å2
2---0.63 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.93→71.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 31 162 3397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193315
X-RAY DIFFRACTIONr_bond_other_d0.0020.023113
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9694516
X-RAY DIFFRACTIONr_angle_other_deg0.99437160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8923.359131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.291527
X-RAY DIFFRACTIONr_chiral_restr0.090.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6462.9831717
X-RAY DIFFRACTIONr_mcbond_other1.6422.9821716
X-RAY DIFFRACTIONr_mcangle_it2.5444.4612142
X-RAY DIFFRACTIONr_mcangle_other2.5444.4612143
X-RAY DIFFRACTIONr_scbond_it2.1553.2321598
X-RAY DIFFRACTIONr_scbond_other2.1543.2341599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3424.7432373
X-RAY DIFFRACTIONr_long_range_B_refined5.39535.753572
X-RAY DIFFRACTIONr_long_range_B_other5.36435.523541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.926→1.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 114 -
Rwork0.243 2540 -
obs--98.66 %
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)
11.03840.32930.67470.760.63591.77030.0595-0.2032-0.0134-0.0545-0.0442-0.0513-0.0043-0.3459-0.01530.04520.0430.00150.1953-0.02540.0351-26.4769-17.202823.4723
20.77320.22990.48830.35070.32531.5796-0.0056-0.0007-0.1582-0.06420.0991-0.0941-0.2655-0.0489-0.09340.08240.0244-0.00150.0803-0.04350.0681-13.5837-15.91711.8052
30.1202-0.2485-0.16753.64151.36060.5641-0.1747-0.00290.14190.0660.4905-0.58690.12580.162-0.31580.2048-0.0242-0.15760.117-0.06690.20229.78233.773138.552
41.0217-0.26110.93452.11610.72171.3215-0.2836-0.2039-0.19620.6610.4679-0.00750.0339-0.0174-0.18430.35590.16750.03070.1622-0.00340.06520.5898-7.828347.2612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 76
2X-RAY DIFFRACTION2A77 - 219
3X-RAY DIFFRACTION3B3 - 92
4X-RAY DIFFRACTION4B93 - 217

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