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- PDB-2fni: PseC aminotransferase involved in pseudoaminic acid biosynthesis -

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Basic information

Entry
Database: PDB / ID: 2fni
TitlePseC aminotransferase involved in pseudoaminic acid biosynthesis
ComponentsaminotransferaseTransaminase
KeywordsTRANSFERASE / aminotransferase / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase / polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase / 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 ...UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase / 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
PYRIDOXAL-5'-PHOSPHATE / : / UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCygler, M. / Matte, A. / Lunin, V.V. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Functional Characterization of PseC, an Aminotransferase Involved in the Biosynthesis of Pseudaminic Acid, an Essential Flagellar Modification in Helicobacter pylori
Authors: Schoenhofen, I.C. / Lunin, V.V. / Julien, J.P. / Li, Y. / Ajamian, E. / Matte, A. / Cygler, M. / Brisson, J.R. / Aubry, A. / Logan, S.M. / Bhatia, S. / Wakarchuk, W.W. / Young, N.M.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aminotransferase
B: aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4124
Polymers84,9172
Non-polymers4942
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-33 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.400, 153.300, 70.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12A
22A

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILE1BB1 - 3741 - 374
21METMETILEILE1AA1 - 3741 - 374
12HOHHOHHOHHOH4AE377
22HOHHOHHOHHOH4AE377

NCS ensembles :
ID
1
2

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Components

#1: Protein aminotransferase / Transaminase


Mass: 42458.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: hp0366 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 2313467, UniProt: O25130*PLUS
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: protein (5 mg/ml) in buffer (20 mM citrate, pH 5.4, 0.1 M NaCl, 5% (v/v) glycerol, and 10 mM DTT) was incubated with 0.5 mM PLP. Crystals of the PseC-PLP complex were grown by mixing 1.5 ...Details: protein (5 mg/ml) in buffer (20 mM citrate, pH 5.4, 0.1 M NaCl, 5% (v/v) glycerol, and 10 mM DTT) was incubated with 0.5 mM PLP. Crystals of the PseC-PLP complex were grown by mixing 1.5 microL protein and 1.5 microL reservoir solution (21% PEG 3350, 0.21 M sodium formate) by vapor diffusion against reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 28, 2004 / Details: Osmic mirrors
RadiationMonochromator: OSMIC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 19466 / Num. obs: 19466 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.1 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FN6

2fn6


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / SU B: 23.027 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25794 996 5.1 %RANDOM
Rwork0.19632 ---
obs0.19943 18470 98.46 %-
all-19466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---2.96 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5921 0 30 21 5972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226079
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9698204
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45124.721269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.776151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4621518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024502
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.32788
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.54225
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.5376
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.52
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.92633781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58855993
X-RAY DIFFRACTIONr_scbond_it1.54742485
X-RAY DIFFRACTIONr_scangle_it2.63282211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
122954tight positional0.030.05
2115medium positional0.520.5
122954tight thermal0.060.5
2115medium thermal0.722
LS refinement shellResolution: 3→3.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 61 -
Rwork0.31 1273 -
obs--92.13 %

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