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- PDB-3ppt: REP1-NXSQ fatty acid transporter -

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Basic information

Entry
Database: PDB / ID: 3ppt
TitleREP1-NXSQ fatty acid transporter
ComponentsReP1-NCXSQ
KeywordsLIPID BINDING PROTEIN / Fatty acid transporter / lipid binding proteins / squid nerve / regulatory factor / Beta-sandwich / Fatty acid
Function / homology
Function and homology information


lipid binding / membrane / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITOLEIC ACID / Sodium/calcium exchanger regulatory protein 1
Similarity search - Component
Biological speciesLoligo pealei (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsBerberian, G. / Bollo, M. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Ayoub, D. / Sanglier-Cianferani, S. / Van Dorsselaer, A. / DiPolo, R. / Beauge, L. ...Berberian, G. / Bollo, M. / Howard, E. / Cousido-Siah, A. / Mitschler, A. / Ayoub, D. / Sanglier-Cianferani, S. / Van Dorsselaer, A. / DiPolo, R. / Beauge, L. / Petrova, T. / Schulze-Briese, C. / Wang, M. / Podjarny, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural and functional studies of ReP1-NCXSQ, a protein regulating the squid nerve Na+/Ca2+ exchanger.
Authors: Cousido-Siah, A. / Ayoub, D. / Berberian, G. / Bollo, M. / Van Dorsselaer, A. / Debaene, F. / DiPolo, R. / Petrova, T. / Schulze-Briese, C. / Olieric, V. / Esteves, A. / Mitschler, A. / ...Authors: Cousido-Siah, A. / Ayoub, D. / Berberian, G. / Bollo, M. / Van Dorsselaer, A. / Debaene, F. / DiPolo, R. / Petrova, T. / Schulze-Briese, C. / Olieric, V. / Esteves, A. / Mitschler, A. / Sanglier-Cianferani, S. / Beauge, L. / Podjarny, A.
History
DepositionNov 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Aug 15, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.4Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: ReP1-NCXSQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0492
Polymers14,7951
Non-polymers2541
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.322, 49.599, 60.492
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 ReP1-NCXSQ


Mass: 14794.868 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C4N147
#2: Chemical ChemComp-PAM / PALMITOLEIC ACID / Palmitoleic acid


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 35% PEG 2000 MME, 0.2 M KCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2008 / Details: MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 31531 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 13.11 Å2 / Rsym value: 0.043 / Net I/σ(I): 32.8
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.376 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIV

1yiv


Resolution: 1.28→30.25 Å / SU ML: 0.13 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.171 1595 5.07 %
Rwork0.134 --
obs0.136 31468 98.6 %
all-31531 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.21 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6833 Å20 Å2-0 Å2
2--3.7952 Å2-0 Å2
3----1.1119 Å2
Refinement stepCycle: LAST / Resolution: 1.28→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 18 252 1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081318
X-RAY DIFFRACTIONf_angle_d1.2911791
X-RAY DIFFRACTIONf_dihedral_angle_d12.371535
X-RAY DIFFRACTIONf_chiral_restr0.078195
X-RAY DIFFRACTIONf_plane_restr0.006238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2805-1.32180.23571270.21392611X-RAY DIFFRACTION96
1.3218-1.3690.23421190.15082686X-RAY DIFFRACTION98
1.369-1.42390.1921450.13272676X-RAY DIFFRACTION99
1.4239-1.48870.18821460.13112674X-RAY DIFFRACTION98
1.4887-1.56710.17971440.1142688X-RAY DIFFRACTION99
1.5671-1.66530.1621560.11122699X-RAY DIFFRACTION99
1.6653-1.79390.17731450.11372727X-RAY DIFFRACTION99
1.7939-1.97440.15161400.12992738X-RAY DIFFRACTION99
1.9744-2.260.1611570.12732767X-RAY DIFFRACTION100
2.26-2.8470.21051770.14532768X-RAY DIFFRACTION100
2.847-30.25440.14141390.1442839X-RAY DIFFRACTION96

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