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- PDB-5i0c: Crystal structure of predicted acyltransferase YjdJ with acyl-CoA... -

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Basic information

Entry
Database: PDB / ID: 5i0c
TitleCrystal structure of predicted acyltransferase YjdJ with acyl-CoA N-acyltransferase domain from Escherichia coli str. K-12
ComponentsUncharacterized protein YjdJ
KeywordsHYDROLASE / coenzyme A / GNAT / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Yjdj-type Gcn5-related N-acetyltransferase / Gcn5-related N-acetyltransferase / GCN5-related N-acetyl-transferase / Yjdj-type Gcn5-related N-acetyltransferase (GNAT) domain profile. / Gcn5-related N-acetyltransferase (GNAT) / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / PHOSPHATE ION / Uncharacterized protein YjdJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsFilippova, E.V. / Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of predicted acyltransferase YjdJ with acyl-CoA N-acyltransferase domain from Escherichia coli str. K-12
Authors: Filippova, E.V. / Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
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.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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YjdJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2386
Polymers10,8541
Non-polymers3835
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.690, 87.840, 41.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized protein YjdJ


Mass: 10854.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yjdJ, b4127, JW4088 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: P39274
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 5 mM Cobalt Chloride, 5 mM Magnesium Chloride, 0.5 mM Cadmium Chloride, 0.5 mM Nickel Chloride, 12 % (w/v) PEG3350, 25 Sucrose, 1 mM AcCoA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.92→30.19 Å / Num. obs: 7731 / % possible obs: 98.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 27.9
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata scaling
PHENIXphasing
PHENIXmodel building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.92→30.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.886 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26595 354 4.6 %RANDOM
Rwork0.21551 ---
obs0.21782 7344 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.871 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å2-0 Å2-0 Å2
2--3.13 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 1.92→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 9 61 793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019737
X-RAY DIFFRACTIONr_bond_other_d0.0020.02731
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.974985
X-RAY DIFFRACTIONr_angle_other_deg1.1831686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.739587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.66824.47438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69415144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.283156
X-RAY DIFFRACTIONr_chiral_restr0.1470.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02810
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02162
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3862.998354
X-RAY DIFFRACTIONr_mcbond_other2.3612.994353
X-RAY DIFFRACTIONr_mcangle_it3.5144.481439
X-RAY DIFFRACTIONr_mcangle_other3.5154.484440
X-RAY DIFFRACTIONr_scbond_it2.4013.267383
X-RAY DIFFRACTIONr_scbond_other2.3273.25380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5524.761541
X-RAY DIFFRACTIONr_long_range_B_refined6.66227.639842
X-RAY DIFFRACTIONr_long_range_B_other6.53923.802819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded41.56552
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.633 31 -
Rwork0.464 506 -
obs--96.24 %
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)
13.3538-0.66541.88457.79419.021612.6044-0.0480.08050.01060.46980.153-0.05460.55470.2326-0.10490.1149-0.0312-0.00510.04170.03590.077641.691920.154530.9989
23.604-1.48651.6817.1415-0.23012.59160.2143-0.134-0.48430.139-0.060.38330.30250.0963-0.15430.1585-0.0053-0.03830.03430.03840.100847.009819.963629.2168
312.6082-10.0132-2.61568.45843.60646.03-0.33760.12260.5290.2175-0.0191-0.257-0.43420.14080.35670.1853-0.0001-0.01090.02140.0270.147645.283234.556331.5338
44.9462-2.1574-5.32087.1218-4.407313.0480.06840.1180.1185-0.3291-0.0608-0.16960.2572-0.1117-0.00760.04730.0345-0.0460.0359-0.05130.094454.268517.903819.2691
55.5692-4.8901-1.48046.7074.61284.95220.01080.4525-0.3455-0.0795-0.22370.4153-0.07160.10410.21290.1582-0.0108-0.02040.09530.04930.131942.715224.986221.2076
612.1981.5871-2.50390.5591-1.23132.8502-0.0410.24670.41910.04440.08220.0492-0.0851-0.1327-0.04120.16370.05580.01130.02920.03060.115135.000835.1728.8292
712.64392.09922.31663.2043-1.71961.9783-0.07970.02610.6512-0.1926-0.1618-0.04440.09130.15330.24160.1626-0.10720.01390.10960.0220.094749.947634.537423.0669
88.9566-2.5263-4.89398.57073.66347.18340.24650.48330.1287-0.384-0.0628-0.0708-0.1854-0.1293-0.18370.21460.0078-0.01310.05160.04530.086243.10637.841518.517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 9
2X-RAY DIFFRACTION2A10 - 28
3X-RAY DIFFRACTION3A29 - 38
4X-RAY DIFFRACTION4A39 - 45
5X-RAY DIFFRACTION5A46 - 60
6X-RAY DIFFRACTION6A61 - 67
7X-RAY DIFFRACTION7A68 - 78
8X-RAY DIFFRACTION8A79 - 91

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