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- PDB-5u23: X-ray structure of the WlaRG aminotransferase from Campylobacter ... -

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Basic information

Entry
Database: PDB / ID: 5u23
TitleX-ray structure of the WlaRG aminotransferase from Campylobacter jejuni in complex with TDP-Qui3N
ComponentsPutative aminotransferase
KeywordsTRANSFERASE / aminotransferase lipooligosaccharide pyridoxal 5'-phosphate
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
Chem-TQP / Putative aminotransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHolden, H.M. / Thoden, J.B. / Dow, G.T. / Gilbert, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Structural investigation on WlaRG from Campylobacter jejuni: A sugar aminotransferase.
Authors: Dow, G.T. / Gilbert, M. / Thoden, J.B. / Holden, H.M.
History
DepositionNov 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Putative aminotransferase
D: Putative aminotransferase
A: Putative aminotransferase
B: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,00919
Polymers176,1784
Non-polymers3,83115
Water28,6981593
1
C: Putative aminotransferase
D: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,15811
Polymers88,0892
Non-polymers2,0699
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-40 kcal/mol
Surface area28720 Å2
MethodPISA
2
A: Putative aminotransferase
B: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8518
Polymers88,0892
Non-polymers1,7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-38 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.824, 56.644, 124.549
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules CDAB

#1: Protein
Putative aminotransferase


Mass: 44044.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetts2(DE3) / References: UniProt: Q9ALS9

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Non-polymers , 6 types, 1608 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-TQP / (2R,3R,4S,5S,6R)-3,5-dihydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 776.471 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H35N4O19P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1593 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPS (pH 7) 12-15% PEG3350 10 mM TDP-Qui3N 1 mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 2, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.383
11-h,-k,l20.617
ReflectionResolution: 1.45→50 Å / Num. obs: 261560 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/av σ(I): 9 / Net I/σ(I): 9
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / Num. unique all: 47910 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2u1z

2u1z


Resolution: 1.45→29.92 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.516 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 12952 5 %RANDOM
Rwork0.12724 ---
obs0.12853 248592 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.901 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å2-1.23 Å2
2--2.34 Å20 Å2
3----4.69 Å2
Refinement stepCycle: 1 / Resolution: 1.45→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11791 0 244 1593 13628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912414
X-RAY DIFFRACTIONr_bond_other_d00.0212036
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.97816818
X-RAY DIFFRACTIONr_angle_other_deg0.796327786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77251483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02925.695590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.364152278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521528
X-RAY DIFFRACTIONr_chiral_restr0.1140.21849
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022808
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_it1.7540.9945859
X-RAY DIFFRACTIONr_mcbond_other1.7510.9935858
X-RAY DIFFRACTIONr_mcangle_it2.2391.497332
X-RAY DIFFRACTIONr_mcangle_other2.2391.4917333
X-RAY DIFFRACTIONr_scbond_it3.0291.3256555
X-RAY DIFFRACTIONr_scbond_other3.0291.3256555
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2881.869474
X-RAY DIFFRACTIONr_long_range_B_refined5.49.70615922
X-RAY DIFFRACTIONr_long_range_B_other5.49.70615922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 899 -
Rwork0.251 17013 -
obs--91.38 %

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