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- PDB-5ykr: Crystal structure of a glutamate-1-semialdehyde-aminomutase from ... -

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Basic information

Entry
Database: PDB / ID: 5ykr
TitleCrystal structure of a glutamate-1-semialdehyde-aminomutase from Pseudomonas aeruginosa PAO1
ComponentsProbable aminotransferase
KeywordsTRANSFERASE / glutamate-1-semialdehyde-aminomutase / C5 pathway
Function / homologyglutamate-1-semialdehyde 2,1-aminomutase activity / Aminotransferase class-III / Aminotransferase class-III / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / Glutamate-1-semialdehyde 2,1-aminomutase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLi, S. / Zhang, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31570128 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of a glutamate-1-semialdehyde-aminomutase from Pseudomonas aeruginosa PAO1.
Authors: Li, S. / Lou, X. / Xu, Y. / Teng, X. / Che, S. / Liu, R. / Bartlam, M.
History
DepositionOct 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable aminotransferase
B: Probable aminotransferase


Theoretical massNumber of molelcules
Total (without water)102,6302
Polymers102,6302
Non-polymers00
Water17,348963
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-58 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.442, 96.497, 100.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 5 - 457 / Label seq-ID: 5 - 457

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable aminotransferase / glutamate-1-semialdehyde-aminomutase


Mass: 51315.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4088 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HWU0, glutamate-1-semialdehyde 2,1-aminomutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 155189 / % possible obs: 100 % / Redundancy: 6.6 % / Net I/σ(I): 23.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0173refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BS8

3bs8


Resolution: 1.44→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.09 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15537 7471 4.9 %RANDOM
Rwork0.12029 ---
obs0.12201 146473 98.49 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 17.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20 Å2
2---0.16 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7086 0 0 963 8049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197306
X-RAY DIFFRACTIONr_bond_other_d0.0020.026650
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9429938
X-RAY DIFFRACTIONr_angle_other_deg1.05315284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51522.291358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.858151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3611578
X-RAY DIFFRACTIONr_chiral_restr0.1110.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218372
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021656
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_it1.3151.4113652
X-RAY DIFFRACTIONr_mcbond_other1.3141.4113651
X-RAY DIFFRACTIONr_mcangle_it1.6962.1254572
X-RAY DIFFRACTIONr_mcangle_other1.6972.1254573
X-RAY DIFFRACTIONr_scbond_it2.1011.7583654
X-RAY DIFFRACTIONr_scbond_other2.1011.7583655
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5782.5255367
X-RAY DIFFRACTIONr_long_range_B_refined3.42519.1918570
X-RAY DIFFRACTIONr_long_range_B_other2.92518.2278296
X-RAY DIFFRACTIONr_rigid_bond_restr2.612313956
X-RAY DIFFRACTIONr_sphericity_free26.4395616
X-RAY DIFFRACTIONr_sphericity_bonded9.966514119
Refine LS restraints NCS

Ens-ID: 1 / Number: 29920 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.442→1.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 475 -
Rwork0.205 8929 -
obs--82.09 %

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