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- PDB-1qou: CEN (Centroradialis) protein from Antirrhinum -

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Basic information

Entry
Database: PDB / ID: 1qou
TitleCEN (Centroradialis) protein from Antirrhinum
ComponentsCEN
KeywordsPLANT PROTEIN / INFLUORESCENCE DETERMINATION IN FLOWERING PLANT MERISTEM / SIGNALLING / MEMBER OF THE PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN FAMILY
Function / homology
Function and homology information


flower development / cell differentiation / cytoplasm
Similarity search - Function
Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein CENTRORADIALIS
Similarity search - Component
Biological speciesANTIRRHINUM MAJUS (snapdragon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBanfield, M.J. / Brady, R.L.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Structure of Antirrhinum Centroradialis Protein (Cen) Suggests a Role as a Kinase Regulator
Authors: Banfield, M.J. / Brady, R.L.
#1: Journal: Structure / Year: 1998
Title: Function from Structure? the Crystal Structure of Human Phosphatidylethanolamine Binding Protein Suggests a Role in Membrane Signal Transduction
Authors: Banfield, M.J. / Barker, J.J. / Perry, A. / Brady, R.L.
#2: Journal: Structure / Year: 1998
Title: Crystal Structure of Bovine Phosphatidylethanolamine-Binding Proteins from Bovine Brain: A Novel Structural Class of Phospholipid-Binding Proteins.
Authors: Serre, L. / Vallee, B. / Bureaud, N. / Schoentgen, F. / Zelwer, C.
History
DepositionNov 17, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CEN
B: CEN


Theoretical massNumber of molelcules
Total (without water)40,7012
Polymers40,7012
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-13.4 kcal/mol
Surface area19100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)40.890, 77.650, 117.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997832, 0.065499, 0.006386), (0.064804, 0.994849, -0.077954), (-0.011459, -0.077371, -0.996937)
Vector: 20.247, -0.203, 10.879)
DetailsIN THE CRYSTAL THE PROTEIN FORMS A HOMO- DIMER THROUGHAN INTER-CHAIN DISULPHIDE BOND. THIS OLIGOMERIC STATEIS NOT EXPECTED TO REPRESENT THE FUNCTIONAL STATE.HOWEVER, A ROLE FOR THIS DIMERIC ASSOCIATION IN PROTEINFUNCTION CANNOT BE RULED OUT .

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Components

#1: Protein CEN


Mass: 20350.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: INTER-MOLECULAR DISULPHIDE BOND FORMED IN THE CRYSTAL, BETWEEN RESIDUES A145 AND B145.
Source: (gene. exp.) ANTIRRHINUM MAJUS (snapdragon) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q41261
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACID NUMBERING: FOR EASE OF COMPARISON, THE NUMBERING SCHEME ADOPTED FOR THIS ENTRY IS BASED ...AMINO ACID NUMBERING: FOR EASE OF COMPARISON, THE NUMBERING SCHEME ADOPTED FOR THIS ENTRY IS BASED ON A SEQUENCE ALIGNMENT OF 38 MEMBERS OF THE PEBP FAMILY. THE HUMAN HOMOLOGUE HAS BEEN TAKEN AS THE REFERENCE (SEE PDB ENTRY 1BD9). ALL AMINO ACID NUMBERING IN THIS ENTRY RELATES TO THE SEQUENCE POSITION IN HUMAN PEBP.

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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: 2.3 Å3/Da / Density % sol: 39.3 %
Crystal growpH: 5.5
Details: 1:1 MIX OF 13MG/ML CEN SOLUTION (10MM HEPES, 50MM NACL. PH 7) WITH 1.8 - 2.1 M NACL BUFFERED WITH 100MM SODIUM ACETATE AT PH 5.4 - 5.6
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMHEPES11
250 mM11NaCl
313 mg/mlprotein11
41.8-2.1 M12NaCl
5100 mMsodium acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 28860 / % possible obs: 94.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.29 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 4.6 / % possible all: 91.4
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BD9

1bd9


Resolution: 1.9→40 Å / SU B: 3.65 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.16
Details: THE REFINED MODEL OF THE A-CHAIN CONTAINS THE FOLLOWING RESIDUES OF THE SEQUENCE LISTED REFINED MODEL OF THE B-CHAIN CONTAINS THE FOLLOWING RESIDUES B32B- B130, B143-B175.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1457 5 %SHELLS
Rwork0.212 ---
obs-27357 94.6 %-
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 0 283 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6072
X-RAY DIFFRACTIONp_mcangle_it2.453
X-RAY DIFFRACTIONp_scbond_it1.7712
X-RAY DIFFRACTIONp_scangle_it2.7513
X-RAY DIFFRACTIONp_plane_restr0.02340.03
X-RAY DIFFRACTIONp_chiral_restr0.01150.03
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor14.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.420
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.212 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / Rfactor obs: 0.259

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