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- PDB-5dud: Crystal structure of E. coli YbgJK -

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Basic information

Entry
Database: PDB / ID: 5dud
TitleCrystal structure of E. coli YbgJK
Components
  • YbgJ
  • YbgK
KeywordsUNKNOWN FUNCTION / protein complex
Function / homology
Function and homology information


5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / ATP binding / cytosol
Similarity search - Function
KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Cyclophilin-like / Cyclophilin / Cyclophilin-like domain superfamily ...KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Cyclophilin-like / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
5-oxoprolinase subunit B / 5-oxoprolinase subunit C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArbing, M.A. / Kaufmann, M. / Shin, A. / Medrano-Soto, A. / Cascio, D. / Eisenberg, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071909-01A2 United States
CitationJournal: To Be Published
Title: Crystal Structure of E. coli YbgJK
Authors: Arbing, M.A. / Kaufmann, M. / Shin, A. / Medrano-Soto, A. / Cascio, D. / Eisenberg, D.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YbgK
B: YbgJ
C: YbgK
D: YbgJ


Theoretical massNumber of molelcules
Total (without water)116,7964
Polymers116,7964
Non-polymers00
Water2,990166
1
A: YbgK
B: YbgJ


Theoretical massNumber of molelcules
Total (without water)58,3982
Polymers58,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-22 kcal/mol
Surface area21180 Å2
MethodPISA
2
C: YbgK
D: YbgJ


Theoretical massNumber of molelcules
Total (without water)58,3982
Polymers58,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.110, 88.780, 83.700
Angle α, β, γ (deg.)90.00, 101.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YbgK


Mass: 34429.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ybgK, b0712, JW0702 / Plasmid: pET46Ek/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P75745
#2: Protein YbgJ


Mass: 23968.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ybgJ, b0711, JW0701 / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AAV4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir solution: 0.1 M Bicine, pH 8.5, 20% PEG 6000. Protein storage buffer: 20 mM Tris-pH 8.0, 300 mM NaCl, 10% glycerol. Additives: TCEP, malonamide.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 23159 / % possible obs: 98.9 % / Redundancy: 3.67 % / Biso Wilson estimate: 71.04 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.43
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.883.770.8090.4782.666466175917140.55797.4
2.88-2.960.8770.3943.156311164516500.459100
2.96-3.040.8990.3094.016181162216180.3699.8
3.04-3.130.9350.2375.346052158515830.27699.9
3.13-3.240.9490.196.65813152315240.222100
3.24-3.350.9680.1448.635741151215040.16799.5
3.35-3.480.9790.12411.064665144614070.14997.3
3.48-3.620.9850.11511.095118136613570.13499.3
3.62-3.780.9860.09514.464173132412650.11595.5
3.78-3.960.9890.0816.424003128412270.09695.6
3.96-4.180.9960.05919.454517120812030.06999.6
4.18-4.430.9960.04923.284279115111440.05799.4
4.43-4.740.9970.04325.493942106710650.0599.8
4.74-5.120.9960.04226.8336719979930.04999.6
5.12-5.610.9960.04325.934689379340.0599.7
5.61-6.270.9970.04325.2330078188180.05100
6.27-7.240.9970.04127.5527357587550.04899.6
7.24-8.870.9980.03131.5122566296250.03699.4
8.87-12.540.9990.02636.6218014964960.031100
12.540.9990.02936.469282832770.03497.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
MR-Rosettaphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MML

3mml


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.8217 / Cor.coef. Fo:Fc free: 0.7726 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.443
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 1185 5.15 %RANDOM
Rwork0.2675 ---
obs0.2685 22991 98.62 %-
Displacement parametersBiso mean: 48.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.078 Å20 Å2-3.5418 Å2
2--3.2709 Å20 Å2
3----5.3489 Å2
Refine analyzeLuzzati coordinate error obs: 0.782 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14165 0 0 166 14331
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00814341HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9525878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3909SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2229HARMONIC5
X-RAY DIFFRACTIONt_it14341HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion3.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion969SEMIHARMONIC5
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_contact14710SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3383 135 4.96 %
Rwork0.3495 2586 -
all0.3489 2721 -
obs--98.62 %
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)
11.4675-0.0796-0.17741.6397-0.66150.75980.0677-0.008-0.0877-0.0214-0.1086-0.05490.0681-0.10150.0409-0.2023-0.0243-0.0561-0.13910.02350.0322-22.370328.215153.5344
27.3584-2.14570.63510.74920.17121.5024-0.02550.11640.1760.06220.00930.0052-0.11310.13660.0162-0.2165-0.0823-0.0096-0.20460.03210.01321.403244.044647.689
32.8863-1.3517-0.89131.2885-0.19831.8525-0.0185-0.28750.00310.00340.0554-0.0182-0.2524-0.0753-0.0368-0.14580.0084-0.0438-0.1461-0.0228-0.09414.113825.197995.0363
40.3888-0.15430.1241.07930.35792.88580.00980.0641-0.1512-0.0186-0.03620.03950.1350.03980.0264-0.18740.0076-0.0811-0.1373-0.01360.080710.66497.998372.0911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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