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- PDB-2gs4: The crystal structure of the E.coli stress protein YciF. -

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Basic information

Entry
Database: PDB / ID: 2gs4
TitleThe crystal structure of the E.coli stress protein YciF.
ComponentsProtein yciF
KeywordsMETAL BINDING PROTEIN / STRESS PROTEINS / RUBRERYTHRIN
Function / homology
Function and homology information


DNA damage response / protein homodimerization activity
Similarity search - Function
: / Protein of unknown function DUF892, YciF-like / Domain of unknown function (DUF892) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHindupur, A. / Liu, D. / Zhao, Y. / Bellamy, H.D. / White, M.A. / Fox, R.O.
CitationJournal: Protein Sci. / Year: 2006
Title: The crystal structure of the E. coli stress protein YciF.
Authors: Hindupur, A. / Liu, D. / Zhao, Y. / Bellamy, H.D. / White, M.A. / Fox, R.O.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein yciF
B: Protein yciF


Theoretical massNumber of molelcules
Total (without water)37,6262
Polymers37,6262
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-15 kcal/mol
Surface area14800 Å2
MethodPISA
2
A: Protein yciF
B: Protein yciF

A: Protein yciF
B: Protein yciF

A: Protein yciF
B: Protein yciF


Theoretical massNumber of molelcules
Total (without water)112,8776
Polymers112,8776
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12890 Å2
ΔGint-61 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.87, 79.87, 131.24
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Protein yciF


Mass: 18812.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 MG1655 / Gene: yciF / Plasmid: p215 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B / References: UniProt: P21362
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M citric acid pH 3.5-4.0, 1.9-2.1M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.9794, 0.9797, 0.9252
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 28, 2004 / Details: Channel Cut Monochromator
RadiationMonochromator: Si(111) Channel Cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97971
30.92521
ReflectionResolution: 2→30 Å / Num. all: 19196 / Num. obs: 19196 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1913 / Rsym value: 0.199 / % possible all: 91.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: RESOLVE

Resolution: 2→29.49 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3476612.91 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 907 4.7 %SHELLS
Rwork0.183 ---
all0.217 19196 --
obs0.183 19178 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9908 Å2 / ksol: 0.398518 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å21.25 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 0 118 2577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 55 5.9 %
Rwork0.402 880 -
obs-880 90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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