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- PDB-1qz4: Structure of YcfC Protein of Unknown Function Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1qz4
TitleStructure of YcfC Protein of Unknown Function Escherichia coli
ComponentsHypothetical protein ycfCHypothesis
KeywordsStructural genomics / unknown function / helix-turn-helix motif / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to heat / plasma membrane / cytoplasm
Similarity search - Function
YcfC-like / HflD-like / High frequency lysogenization protein HflD / HflD-like superfamily / Protein of unknown function (DUF489) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / High frequency lysogenization protein HflD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsOtwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a hypothetical protein ycfC coded by Escherichia coli genome.
Authors: Otwinowski, Z. / Borek, D.M. / Chen, Y. / Skarina, T. / Savchenko, A. / Edwards, A.
History
DepositionSep 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ycfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,99812
Polymers22,8971
Non-polymers2,10111
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.102, 62.749, 68.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein ycfC / Hypothesis / ORF-23


Mass: 22897.371 Da / Num. of mol.: 1 / Fragment: ycfC protein / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YCFC / Production host: Escherichia coli (E. coli) / References: UniProt: P25746
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, zinc acetate, lithium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.999871
SYNCHROTRONAPS 19-ID20.91963
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDAug 24, 2003
CUSTOM-MADE2CCDJun 21, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL MONOCHROMATOR SI-220SINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL MONOCHROMATOR SI-220SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9998711
20.919631
ReflectionResolution: 1.95→50 Å / Num. all: 13895 / Num. obs: 11477 / % possible obs: 82.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.87
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.8 / % possible all: 36.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS
Starting model: Build by WARP/ARP

Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.947 / SU B: 2.014 / SU ML: 0.058 / σ(F): 0 / ESU R: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
all0.15729 11138 -
obs0.15729 11138 85.24 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2--0.8 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 15 111 1731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211620
X-RAY DIFFRACTIONr_bond_other_d0.0020.021543
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9742197
X-RAY DIFFRACTIONr_angle_other_deg0.91133567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685212
X-RAY DIFFRACTIONr_chiral_restr0.0910.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021805
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02302
X-RAY DIFFRACTIONr_nbd_refined0.230.2390
X-RAY DIFFRACTIONr_nbd_other0.2310.21704
X-RAY DIFFRACTIONr_nbtor_other0.0860.2976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.282
X-RAY DIFFRACTIONr_metal_ion_refined0.3670.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.211
X-RAY DIFFRACTIONr_mcbond_it5.32121054
X-RAY DIFFRACTIONr_mcangle_it6.4731679
X-RAY DIFFRACTIONr_scbond_it7.5482566
X-RAY DIFFRACTIONr_scangle_it9.3923518
X-RAY DIFFRACTIONr_sphericity_free11.153210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.148 400
Rfree-0

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