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

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Basic information

Entry
Database: PDB / ID: 5nlc
TitleStructure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942,without PLP
ComponentsPipY
KeywordsPLP-binding protein / modified TIM barrel / fold type III PLP-protein / vitamin B6 / pyridoxal phosphate
Function / homology
Function and homology information


pyridoxal phosphate binding / metal ion 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
PHOSPHATE ION / Pyridoxal phosphate homeostasis protein
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 4, 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 2.0May 2, 2018Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Polymer sequence / Refinement description
Category: entity_poly / pdbx_audit_support ...entity_poly / pdbx_audit_support / refine / reflns / reflns_shell
Item: _entity_poly.pdbx_target_identifier / _refine.pdbx_starting_model ..._entity_poly.pdbx_target_identifier / _refine.pdbx_starting_model / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PipY
B: PipY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6953
Polymers50,6002
Non-polymers951
Water6,756375
1
A: PipY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3952
Polymers25,3001
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PipY


Theoretical massNumber of molelcules
Total (without water)25,3001
Polymers25,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.618, 41.778, 77.761
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PipY


Mass: 25299.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence provided has a C-terminal His6 tag
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 1.97 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5 0.2 M Magnesium chloride 25% (wt/vol) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→44.61 Å / Num. obs: 32801 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.023 / Net I/σ(I): 20.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4 / Num. unique obs: 2072 / CC1/2: 0.935 / Rpim(I) all: 0.17 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w8g

1w8g


Resolution: 1.9→44.61 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.08 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.20744 1632 5 %RANDOM
Rwork0.15719 ---
obs0.15963 31157 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0.38 Å2
2--0.59 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 5 375 3693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193423
X-RAY DIFFRACTIONr_bond_other_d0.0020.023253
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9634664
X-RAY DIFFRACTIONr_angle_other_deg1.04337528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07524.04151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13715578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.041528
X-RAY DIFFRACTIONr_chiral_restr0.1070.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213828
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02672
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_it1.1111.5441734
X-RAY DIFFRACTIONr_mcbond_other1.1051.5421733
X-RAY DIFFRACTIONr_mcangle_it1.7842.3082167
X-RAY DIFFRACTIONr_mcangle_other1.7852.3092168
X-RAY DIFFRACTIONr_scbond_it1.71.811689
X-RAY DIFFRACTIONr_scbond_other1.6871.7991686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.732.6052486
X-RAY DIFFRACTIONr_long_range_B_refined4.9819.4833790
X-RAY DIFFRACTIONr_long_range_B_other4.81918.6683689
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 117 -
Rwork0.2 2237 -
obs--99.07 %
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)
11.17260.4134-1.00460.5948-0.99754.0487-0.0220.1051-0.03290.00050.1354-0.01560.0828-0.3683-0.11340.0079-0.0081-0.00320.17530.0350.0354-4.634-10.61937.389
21.17570.30180.05020.3638-0.44620.75540.0133-0.0710.01330.03590.00510.0132-0.06850.0021-0.01840.0455-0.0068-0.01270.1489-0.01970.030913.7380.60535.924
36.9871-3.0724-0.08261.7729-0.08261.2293-0.04790.06950.1672-0.05780.0439-0.0522-0.04730.15480.00390.0266-0.0240.00830.1485-0.00680.03447.9521.45519.383
40.9699-0.0277-0.58931.4033-0.45933.45180.0515-0.0185-0.1166-0.01220.08320.0855-0.0438-0.1911-0.13470.0117-0.0095-0.00930.16160.01840.0384-1.396-3.94327.911
51.1465-1.1228-0.7061.7001-0.2455.79190.12830.00710.01870.16150.1981-0.0972-0.17040.4427-0.32630.18850.1155-0.0690.2513-0.11540.0633-7.555-8.2954.979
63.6893-1.9006-0.27791.7220.73360.71690.16070.38380.0558-0.0659-0.115-0.0402-0.08320.0236-0.04570.04180.03470.01040.1999-0.00210.0111-19.784-3.475-3.982
70.56780.70651.15562.32471.48462.79070.0192-0.05310.0113-0.0558-0.00760.0603-0.0263-0.1155-0.01150.01570.0083-0.0020.17930.01210.0311-32.1430.3626.759
81.31590.56590.26180.48820.64531.2160.03590.05210.03060.06420.0381-0.02340.10550.0237-0.07410.03560.0119-0.00860.1584-0.00930.0372-19.228-2.06915.522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 45
2X-RAY DIFFRACTION2A46 - 153
3X-RAY DIFFRACTION3A154 - 186
4X-RAY DIFFRACTION4A187 - 218
5X-RAY DIFFRACTION5B3 - 32
6X-RAY DIFFRACTION6B33 - 96
7X-RAY DIFFRACTION7B97 - 150
8X-RAY DIFFRACTION8B151 - 217

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