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- PDB-5u21: X-ray structure of the WlaRF aminotransferase from Campylobacter ... -

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Basic information

Entry
Database: PDB / ID: 5u21
TitleX-ray structure of the WlaRF aminotransferase from Campylobacter jejuni, K184A mutant in complex with TDP-Qui3N
ComponentsPutative aminotransferaseTransaminase
KeywordsTRANSFERASE / aminotransferase / pyridoxal 5'-phosphate / lipooligosaccharide
Function / homology
Function and homology information


transaminase activity
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: 1.6 Å
AuthorsThoden, J.B. / Holden, H.M. / 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 / Structure summary / Category: pdbx_audit_support / struct_keywords
Item: _pdbx_audit_support.funding_organization / _struct_keywords.pdbx_keywords
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)179,50517
Polymers175,9464
Non-polymers3,56013
Water28,7161594
1
A: Putative aminotransferase
B: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,83310
Polymers87,9732
Non-polymers1,8608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-40 kcal/mol
Surface area27880 Å2
MethodPISA
2
C: Putative aminotransferase
D: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6737
Polymers87,9732
Non-polymers1,7005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-37 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.164, 56.653, 124.802
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative aminotransferase / Transaminase


Mass: 43986.430 Da / Num. of mol.: 4 / Mutation: K184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9ALS9

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Non-polymers , 5 types, 1607 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1594 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM MOPS (pH 7) 12-15% PEG-3350 1 mM PLP 10 mM TDP-Qui3N

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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: Aug 21, 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, L10.396
11-h,-k,l20.604
ReflectionResolution: 1.6→50 Å / Num. obs: 194888 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 10.2 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.9 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5u1z

5u1z


Resolution: 1.6→29.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.937 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16132 9738 5 %RANDOM
Rwork0.13222 ---
obs0.13369 185140 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.422 Å2
Baniso -1Baniso -2Baniso -3
1-7.16 Å20 Å2-3.35 Å2
2--0.49 Å20 Å2
3----7.64 Å2
Refinement stepCycle: 1 / Resolution: 1.6→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11714 0 227 1594 13535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912252
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211855
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.97616593
X-RAY DIFFRACTIONr_angle_other_deg0.855327348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85751461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72825.719584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2021528
X-RAY DIFFRACTIONr_chiral_restr0.120.21826
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022773
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_it2.051.3595808
X-RAY DIFFRACTIONr_mcbond_other2.0491.3585807
X-RAY DIFFRACTIONr_mcangle_it2.5862.047263
X-RAY DIFFRACTIONr_mcangle_other2.5862.047264
X-RAY DIFFRACTIONr_scbond_it3.0021.6776444
X-RAY DIFFRACTIONr_scbond_other3.0011.6776444
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2542.3899325
X-RAY DIFFRACTIONr_long_range_B_refined5.61512.56715732
X-RAY DIFFRACTIONr_long_range_B_other5.61512.56715733
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 614 -
Rwork0.261 12543 -
obs--89.53 %

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