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- PDB-3uwc: Structure of an aminotransferase (DegT-DnrJ-EryC1-StrS family) fr... -

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Basic information

Entry
Database: PDB / ID: 3uwc
TitleStructure of an aminotransferase (DegT-DnrJ-EryC1-StrS family) from Coxiella burnetii in complex with PMP
ComponentsNucleotide-sugar aminotransferase
KeywordsTRANSFERASE / lipopolysaccharide biosynthesis
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Nucleotide-sugar aminotransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCheung, J. / Franklin, M. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionDec 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotide-sugar aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2797
Polymers42,8111
Non-polymers4676
Water7,152397
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleotide-sugar aminotransferase
hetero molecules

A: Nucleotide-sugar aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,55814
Polymers85,6232
Non-polymers93512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7720 Å2
ΔGint-76 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.899, 76.899, 144.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-374-

NA

21A-673-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nucleotide-sugar aminotransferase


Mass: 42811.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0696 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B5U8Q1, Transferases; Transferring nitrogenous groups; Transaminases

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Non-polymers , 5 types, 403 molecules

#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 10% dioxane, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 41059 / Num. obs: 40977 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.064 / Χ2: 1.051 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.835.70.61119860.674198.2
1.83-1.865.80.51719840.676199.1
1.86-1.960.45620000.697199.5
1.9-1.946.40.39519890.748199.7
1.94-1.986.90.33220500.821100
1.98-2.037.50.26520200.8661100
2.03-2.088.20.21620250.9721100
2.08-2.138.90.19220120.961100
2.13-2.29.10.16320280.9671100
2.2-2.279.50.14220360.9861100
2.27-2.35100.12720300.9951100
2.35-2.4410.70.11820271.0071100
2.44-2.5512.20.10520501.0121100
2.55-2.69130.09420411.0381100
2.69-2.8613.10.07720731.0331100
2.86-3.08130.06220691.0131100
3.08-3.39130.04920581.0141100
3.39-3.8812.80.04321101.3541100
3.88-4.8812.50.04221311.728199.9
4.88-3010.70.03722581.303198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FRK

3frk


Resolution: 1.8→27.997 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8854 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 2047 5.01 %RANDOM
Rwork0.1673 ---
all0.1683 43057 --
obs0.1683 40821 99.56 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.989 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 73.28 Å2 / Biso mean: 24.8721 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.3117 Å20 Å2-0 Å2
2--3.3117 Å2-0 Å2
3----6.6234 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 29 397 3391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063170
X-RAY DIFFRACTIONf_angle_d0.9644309
X-RAY DIFFRACTIONf_chiral_restr0.067470
X-RAY DIFFRACTIONf_plane_restr0.004563
X-RAY DIFFRACTIONf_dihedral_angle_d12.3751175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84190.28411300.25332522265298
1.8419-1.8880.25911240.22342520264499
1.888-1.9390.23811370.198425162653100
1.939-1.99610.1971500.181825412691100
1.9961-2.06050.20941420.156325562698100
2.0605-2.13410.17251220.15525832705100
2.1341-2.21950.19871400.150225502690100
2.2195-2.32050.17721350.147725862721100
2.3205-2.44270.20481700.163725182688100
2.4427-2.59570.21641290.16822573270299
2.5957-2.79590.16781190.16812594271399
2.7959-3.0770.14791370.15582609274699
3.077-3.52150.18241240.165726342758100
3.5215-4.43390.15551590.15126382797100
4.4339-27.9970.21251290.18192834296399
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)
10.47170.0411-0.35380.60570.14520.5145-0.0741-0.01940.1952-0.02490.0923-0.2866-0.14370.1427-0.01880.2321-0.037-0.02520.2135-0.04460.274324.556531.71277.4738
20.1515-0.07680.1160.29150.04840.1841-0.0077-0.0433-0.00520.06150.0215-0.03380.0263-0.0128-0.00330.0985-0.0048-0.01030.1122-0.00840.1115.293515.44598.2101
30.07560.2384-0.06110.70810.07370.4258-0.0453-0.0516-0.06530.1529-0.01230.28530.1043-0.26980.01460.157-0.01350.0260.23140.00020.2038-9.170719.057110.5588
40.07010.0740.06450.1860.11720.0502-0.1174-0.0111-0.02020.11070.155-0.0099-0.0292-0.2788-0.0540.11760.00310.01830.1872-0.00010.0825-3.257823.523716.8552
50.4032-0.10330.00760.64250.52970.4284-0.0594-0.05150.03970.06670.0574-0.0686-0.0022-0.03190.00150.17530.0075-0.00560.1626-0.00310.13119.946620.758514.4594
6-0.2896-0.16550.0840.51940.12120.0019-0.0558-0.0913-0.01520.04040.0577-0.0307-0.04640.0644-0.00930.2062-0.0038-0.00340.1718-0.02170.205716.884127.547410.6063
70.56920.0086-0.06090.63670.15440.1413-0.081-0.01120.0705-0.09110.01990.056-0.1151-0.13280.02560.2220.0456-0.05020.168-0.0080.1691-4.360343.28245.4906
80.2447-0.02050.13710.6480.03810.501-0.03450.0142-0.1288-0.13090.01890.0599-0.0345-0.21080.00320.13630.0071-0.02350.1824-0.01360.1752-6.068228.296-3.3037
90.5663-0.36910.2720.52830.24140.6469-0.0906-0.05440.0917-0.0976-0.0074-0.0294-0.2866-0.14220.04620.22610.0338-0.02870.1795-0.01640.1841-1.4639.15813.0201
100.6635-0.2829-0.16790.1963-0.1250.47190.00510.06030.8323-0.1429-0.0654-0.0479-0.65810.00620.14140.42650.1063-0.09240.1340.01880.3667-2.30654.84420.3278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:48)A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:94)A49 - 94
3X-RAY DIFFRACTION3chain 'A' and (resseq 95:126)A95 - 126
4X-RAY DIFFRACTION4chain 'A' and (resseq 127:147)A127 - 147
5X-RAY DIFFRACTION5chain 'A' and (resseq 148:211)A148 - 211
6X-RAY DIFFRACTION6chain 'A' and (resseq 212:262)A212 - 262
7X-RAY DIFFRACTION7chain 'A' and (resseq 263:301)A263 - 301
8X-RAY DIFFRACTION8chain 'A' and (resseq 302:330)A302 - 330
9X-RAY DIFFRACTION9chain 'A' and (resseq 331:350)A331 - 350
10X-RAY DIFFRACTION10chain 'A' and (resseq 351:371)A351 - 371

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