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- PDB-2uxv: SufI Protein from Escherichia Coli -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2uxv
TitleSufI Protein from Escherichia Coli
ComponentsPROTEIN SUFI
KeywordsOXIDOREDUCTASE / SUFI / PERIPLASMIC / CUPREDOXIN-LIKE / FTS MUTANT SUPPRESSOR
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / response to ionizing radiation / cell division site / outer membrane-bounded periplasmic space / response to oxidative stress / oxidoreductase activity / copper ion binding / cell division
Similarity search - Function
Cell division protein FtsP / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. ...Cell division protein FtsP / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell division protein FtsP
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsTarry, M.J. / Roversi, P. / Sargent, F. / Berks, B.C. / Lea, S.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The Escherichia Coli Cell Division Protein and Model Tat Substrate Sufi (Ftsp) Localizes to the Septal Ring and Has a Multicopper Oxidase-Like Structure.
Authors: Tarry, M. / Arends, S.J. / Roversi, P. / Piette, E. / Sargent, F. / Berks, B.C. / Weiss, D.S. / Lea, S.M.
History
DepositionMar 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN SUFI
B: PROTEIN SUFI


Theoretical massNumber of molelcules
Total (without water)100,4902
Polymers100,4902
Non-polymers00
Water1,11762
1
A: PROTEIN SUFI


Theoretical massNumber of molelcules
Total (without water)50,2451
Polymers50,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEIN SUFI


Theoretical massNumber of molelcules
Total (without water)50,2451
Polymers50,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.120, 48.880, 131.960
Angle α, β, γ (deg.)90.00, 95.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.996, 0.086, -0.008), (0.085, 0.994, 0.075), (0.015, 0.074, -0.997)
Vector: -56.88804, 4.51364, -64.19139)

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Components

#1: Protein PROTEIN SUFI / SUFI


Mass: 50244.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: P60-SUFI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: P26648
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.44 % / Description: NONE
Crystal growpH: 8.5 / Details: 2.35M NACL 0.1M IMIDAZOLE, PH 8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→64 Å / Num. obs: 24830 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 1.06 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.7 / % possible all: 96.8

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Processing

Software
NameVersionClassification
TNT5.13.1.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UXT

2uxt


Resolution: 2.61→59.76 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: STRUCTURE REFINED IN BUSTERTNT VERSION BETA 2.1.1
RfactorNum. reflection
Rwork0.214 -
all0.2156 24819
obs0.214 24819
Solvent computationSolvent model: BABINET SCALING / Bsol: 65 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 2.61→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 0 62 6683
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00568092
X-RAY DIFFRACTIONt_angle_deg1.1992302
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0081762
X-RAY DIFFRACTIONt_gen_planes0.0169815
X-RAY DIFFRACTIONt_it1.357680920
X-RAY DIFFRACTIONt_nbd0.0811665
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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