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- PDB-2q4u: Ensemble refinement of the crystal structure of an EF-hand protei... -

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Basic information

Entry
Database: PDB / ID: 2q4u
TitleEnsemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843
ComponentsProtein Zgc:100843
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / Dr.36843 / BC083168 / CALICIUM BINDING / EF-HAND SUPERFAMILY / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


spinal cord motor neuron differentiation / regulation of presynaptic cytosolic calcium ion concentration / regulation of long-term synaptic potentiation / brain development / terminal bouton / dendrite / synapse / calcium ion binding / nucleus / cytosol
Similarity search - Function
Secretagogin, EF-hand domain / : / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Secretagogin, EF-hand domain / : / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.1 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Zgc:100843


Theoretical massNumber of molelcules
Total (without water)32,0501
Polymers32,0501
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.884, 52.748, 114.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Number of models16

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Components

#1: Protein Protein Zgc:100843


Mass: 32050.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Strain: Singapore local strain / Gene: Dr.36843, BC083168, zgc:100843 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q5XJX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.9 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2BE4.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2BE4

2be4


Resolution: 2.1→44.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1451262.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2be4 and the first data set in the deposited structure factor file for 2be4 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2be4 and the first data set in the deposited structure factor file for 2be4 along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 885 5.1 %RANDOM
Rwork0.154 ---
obs0.154 17332 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.004 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å20 Å20 Å2
2---4 Å20 Å2
3----0.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 240 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.230.2651505.40.15826370.0222847278797.9
2.23-2.40.2291445.10.12826840.0192881282898.1
2.4-2.650.2551475.20.15827050.0212890285298.7
2.65-3.030.3121555.40.16727130.0252891286899.2
3.03-3.820.2441515.20.16727730.022948292499.2
3.82-44.170.2111384.50.14629350.0183088307399.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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