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- PDB-2g0y: Crystal Structure of a Lumenal Pentapeptide Repeat Protein from C... -

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Basic information

Entry
Database: PDB / ID: 2g0y
TitleCrystal Structure of a Lumenal Pentapeptide Repeat Protein from Cyanothece sp 51142 at 2.3 Angstrom Resolution. Tetragonal Crystal Form
Componentspentapeptide repeat protein
KeywordsUNKNOWN FUNCTION / Right-Handed Beta Helix
Function / homologyThylakoid lumenal 15kDa protein 1-like / plasma membrane-derived thylakoid lumen / Pentapeptide repeats (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Pentapeptide repeat protein Rfr32
Function and homology information
Biological speciesCyanothece sp. ATCC 51142 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKennedy, M.A. / Ni, S. / Buchko, G.W. / Robinson, H.
CitationJournal: Protein Sci. / Year: 2006
Title: Characterization of two potentially universal turn motifs that shape the repeated five-residues fold - Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142
Authors: Buchko, G.W. / Ni, S. / Robinson, H. / Welsh, E.A. / Pakrasi, H.B. / Kennedy, M.A.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_atom_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_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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS FILE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pentapeptide repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9114
Polymers19,7911
Non-polymers1203
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.614, 86.614, 89.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-155-

HOH

DetailsSingle molecule in asymmetric unit is thought to be biological assembly

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Components

#1: Protein pentapeptide repeat protein


Mass: 19790.908 Da / Num. of mol.: 1
Fragment: full-length pentapeptide repeat protein minus N-terminal 29 residues predicted to be a signal peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. ATCC 51142 (bacteria) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: UniProt: B1WVN5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 4000, 0.1 M magnesium chloride, 5% glycerol, .06 M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2005
Details: Rosenbaum-Rock double crystal saggital focusing monochometer and vertical focusing mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→500 Å / Num. all: 7884 / Num. obs: 7560 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 25.56
Reflection shellHighest resolution: 2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.36 / Num. unique all: 685 / Rsym value: 0.205 / % possible all: 89.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F3L

2f3l


Resolution: 2.3→500 Å / Isotropic thermal model: isotropic / Cross valid method: random / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 382 -random
Rwork0.2329 ---
all0.2329 7884 --
obs0.2329 7357 93.3 %-
Displacement parametersBiso mean: 36.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 3 16 1013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.064
LS refinement shellHighest resolution: 2.3 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.2655 382 -
Rwork0.2329 --
obs-7582 93.3 %

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