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- PDB-3c0u: Crystal structure of E.coli yaeQ protein -

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Basic information

Entry
Database: PDB / ID: 3c0u
TitleCrystal structure of E.coli yaeQ protein
ComponentsUncharacterized protein yaeQ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Escherichia coli / yaeQ / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Restriction endonuclease-like alpha-beta roll fold / Restriction endonuclease-like alpha-beta roll domain / YaeQ / YaeQ superfamily / YaeQ protein / YaeQ / Restriction endonuclease type II-like / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YaeQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsChang, C. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of E.coli yaeQ protein.
Authors: Chang, C. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 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 / struct_site
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 / _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: Uncharacterized protein yaeQ
B: Uncharacterized protein yaeQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6885
Polymers42,4612
Non-polymers2283
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein yaeQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3262
Polymers21,2301
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uncharacterized protein yaeQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3623
Polymers21,2301
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.277, 127.277, 72.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Uncharacterized protein yaeQ


Mass: 21230.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yaeQ, b0190, JW0186 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: P0AA97
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Sodium cacodylate pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 16762 / Num. obs: 16728 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15.7 % / Biso Wilson estimate: 85.413 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 55.36
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1619 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→44.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 19.747 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.477 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 843 5.1 %RANDOM
Rwork0.20954 ---
all0.21079 16675 --
obs0.21079 16675 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.386 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 11 38 2897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9313972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7324.73148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9431520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022222
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21079
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21921
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6891.51836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97522836
X-RAY DIFFRACTIONr_scbond_it1.31931281
X-RAY DIFFRACTIONr_scangle_it2.1484.51136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 68 -
Rwork0.328 1138 -
obs-1206 99.26 %
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)
12.4910.47150.57173.01250.28323.23470.00580.4625-0.5262-0.34420.1278-0.57620.40740.2744-0.1335-0.11510.1107-0.0025-0.0678-0.0697-0.026823.565639.2168-18.3311
213.10812.09493.04597.25571.04421.44360.34050.19-0.5042-0.04360.079-0.62140.8986-0.0735-0.4195-0.07940.02480.0018-0.0751-0.0645-0.133817.960242.3485-17.1458
32.97911.99240.26567.17361.04192.7025-0.08820.37410.1472-0.39150.11590.3668-0.1445-0.2323-0.0276-0.17630.0480.0125-0.09520.011-0.226716.119452.4638-19.1894
42.46680.03660.17861.95610.07741.8645-0.1610.21240.4173-0.12590.05890.3471-0.2798-0.01840.1021-0.00470.03670.0299-0.07740.03640.035143.810927.5544-15.5829
514.05072.2546-4.36964.5327-1.48071.50460.41510.14710.61060.2185-0.16410.3181-0.43910.1399-0.2510.00680.04590.0124-0.00450.0462-0.034448.804823.533-14.271
62.06151.8631-0.37084.5323-0.65432.5356-0.0570.2476-0.1835-0.10870.146-0.26720.19640.182-0.089-0.05890.0506-0.01210.0094-0.013-0.031349.401813.3124-15.9869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 333 - 35
2X-RAY DIFFRACTION1AA149 - 180151 - 182
3X-RAY DIFFRACTION2AA34 - 5336 - 55
4X-RAY DIFFRACTION3AA54 - 14856 - 150
5X-RAY DIFFRACTION4BB1 - 333 - 35
6X-RAY DIFFRACTION4BB149 - 180151 - 182
7X-RAY DIFFRACTION5BB34 - 5336 - 55
8X-RAY DIFFRACTION6BB54 - 14856 - 150

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