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- PDB-5u1z: X-ray structure of the WlarG aminotransferase, apo form, from Cam... -

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Basic information

Entry
Database: PDB / ID: 5u1z
TitleX-ray structure of the WlarG aminotransferase, apo form, from Campylobacter jejune
ComponentsPutative aminotransferase
KeywordsTRANSFERASE / aminotransferase / PLP / lipooligosaccharide
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
Putative aminotransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.4Oct 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.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

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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)176,3309
Polymers176,1784
Non-polymers1525
Water12,827712
1
A: Putative aminotransferase
B: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1835
Polymers88,0892
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-47 kcal/mol
Surface area28460 Å2
MethodPISA
2
C: Putative aminotransferase
D: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1484
Polymers88,0892
Non-polymers582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-40 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.726, 56.837, 124.797
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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): Rosetta2(DE3) / References: UniProt: Q9ALS9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 43.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM MOPS (pH 7) 18-18% PEG-3350

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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: Jul 1, 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, L10.513
11h,-k,-l20.487
ReflectionResolution: 1.6→50 Å / Num. obs: 197128 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/av σ(I): 8.4 / Net I/σ(I): 8.4
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2 / Num. unique all: 31639 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3frk

3frk


Resolution: 1.6→29.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 0.975 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.017 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18768 9871 5 %RANDOM
Rwork0.14833 ---
obs0.15032 187240 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.501 Å2
Baniso -1Baniso -2Baniso -3
1-4.65 Å20 Å2-1.27 Å2
2--1.72 Å20 Å2
3----6.37 Å2
Refinement stepCycle: 1 / Resolution: 1.6→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11705 0 5 712 12422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912008
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211749
X-RAY DIFFRACTIONr_angle_refined_deg1.741.95716230
X-RAY DIFFRACTIONr_angle_other_deg0.83327098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3851456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00625.695583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.259152254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111529
X-RAY DIFFRACTIONr_chiral_restr0.1110.21791
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213552
X-RAY DIFFRACTIONr_gen_planes_other00.022743
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_it1.7971.1385782
X-RAY DIFFRACTIONr_mcbond_other1.7971.1385781
X-RAY DIFFRACTIONr_mcangle_it2.3811.7077225
X-RAY DIFFRACTIONr_mcangle_other2.3811.7087226
X-RAY DIFFRACTIONr_scbond_it2.571.4196226
X-RAY DIFFRACTIONr_scbond_other2.571.426227
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6192.0268997
X-RAY DIFFRACTIONr_long_range_B_refined4.6489.84814102
X-RAY DIFFRACTIONr_long_range_B_other4.6429.75913858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 680 -
Rwork0.264 12960 -
obs--92.94 %

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