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- PDB-4eru: Crystal Structure of Putative Cytoplasmic Protein, YciF Bacterial... -

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Basic information

Entry
Database: PDB / ID: 4eru
TitleCrystal Structure of Putative Cytoplasmic Protein, YciF Bacterial Stress Response Protein from Salmonella enterica
ComponentsYciF Bacterial Stress Response Protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP / helix-bundle / ferritin-like domain
Function / homology
Function and homology information


: / 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
D-MALATE / Putative cytoplasmic protein / Putative cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, Y. / Wu, R. / Jedrzejczak, R. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: Crystal Structure of Putative Cytoplasmic Protein, YciF Bacterial Stress Response Protein from Salmonella enterica
Authors: Kim, Y. / Wu, R. / Jedrzejczak, R. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YciF Bacterial Stress Response Protein
B: YciF Bacterial Stress Response Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5488
Polymers38,1822
Non-polymers3656
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-45 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.138, 107.138, 59.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein YciF Bacterial Stress Response Protein


Mass: 19091.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028S / Gene: yciF, STM14_2092 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D0ZIZ7, UniProt: A0A0F6B221*PLUS
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis Tris Propane pH 7.0, 2.4 M D/L Malic acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2011 / Details: mittors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 23043 / Num. obs: 23043 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 39.56 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1152 / Rsym value: 0.634 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→36.686 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.81 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1182 5.14 %random
Rwork0.173 ---
all0.175 22997 --
obs0.175 22997 99.88 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.545 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 54.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.0748 Å2-0 Å2-0 Å2
2--7.0748 Å20 Å2
3----14.1495 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 22 120 2615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152701
X-RAY DIFFRACTIONf_angle_d1.3713661
X-RAY DIFFRACTIONf_dihedral_angle_d17.8751059
X-RAY DIFFRACTIONf_chiral_restr0.088427
X-RAY DIFFRACTIONf_plane_restr0.006488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1004-2.1960.2581610.211427022863
2.196-2.31170.26031390.187426952834
2.3117-2.45650.21541520.182927102862
2.4565-2.64620.22381410.172527082849
2.6462-2.91230.25461700.192127082878
2.9123-3.33350.24821470.178327352882
3.3335-4.19890.19931360.157427542890
4.1989-36.69160.20451360.168628032939
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.44972.02281.08882.50781.4364.6110.0371-0.45470.5610.0437-0.31820.3683-0.4922-0.29870.17790.3962-0.0084-0.00390.4476-0.02770.3966-28.704666.8034.3152
22.93790.99181.02852.5413-0.22524.44520.0603-0.15660.04250.0831-0.19470.0521-0.0449-0.45570.10210.348-0.00830.01640.4665-0.02830.4382-31.403658.9471-2.6501
31.92421.19260.59941.91-0.03755.33850.0142-0.1757-0.12020.1884-0.2033-0.11180.05140.11240.06490.31620.0046-0.00080.37190.01410.3817-22.185262.3523-4.3252
42.11170.03430.09582.94470.61415.74110.1031-0.202-0.33930.1754-0.1379-0.40660.70980.42270.05780.38370.0029-0.01780.4210.0910.5159-18.983555.0132-1.776
50.8631.41851.08494.37912.03844.0097-0.1323-0.08250.3009-0.4659-0.27460.5684-0.3302-0.58490.27190.42420.0221-0.03260.4368-0.01460.4007-22.55673.9775-18.3421
62.50961.0106-0.02763.19421.50443.6621-0.1292-0.05380.067-0.1814-0.03620.0614-0.4413-0.17250.16370.4810.0008-0.05250.38490.03820.4697-15.879578.4694-11.6571
71.21410.90790.33842.77880.99644.2307-0.0057-0.1622-0.08720.0323-0.2133-0.1242-0.00460.02470.07770.2887-0.017-0.01520.38720.01530.3887-16.720669.3191-8.4977
82.04851.37511.01463.23810.61025.49930.0519-0.1162-0.37460.03110.0265-0.6892-0.09710.59130.02740.37780.0205-0.00250.45640.02410.5474-8.657467.58-11.2053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:34)A0 - 34
2X-RAY DIFFRACTION2chain 'A' and (resseq 35:95)A35 - 95
3X-RAY DIFFRACTION3chain 'A' and (resseq 96:127)A96 - 127
4X-RAY DIFFRACTION4chain 'A' and (resseq 128:158)A128 - 158
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:34)B1 - 34
6X-RAY DIFFRACTION6chain 'B' and (resseq 35:95)B35 - 95
7X-RAY DIFFRACTION7chain 'B' and (resseq 96:127)B96 - 127
8X-RAY DIFFRACTION8chain 'B' and (resseq 128:158)B128 - 158

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