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- PDB-6hx7: Crystal structure of human R180T variant of ORNITHINE AMINOTRANSF... -

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Basic information

Entry
Database: PDB / ID: 6hx7
TitleCrystal structure of human R180T variant of ORNITHINE AMINOTRANSFERASE at 1.8 Angstrom
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE / AMINOTRANSFERASE
Function / homology
Function and homology information


arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGiardina, G. / Montioli, R. / Cellini, B. / Cutruzzola, F. / Borri Voltattorni, C.
Funding support Italy, 2items
OrganizationGrant numberCountry
Other privateTelethon Grant GGP15114 to B. Cellini Italy
European Communitys Seventh Framework Programmegrant agreement n. 312284 Italy
CitationJournal: Febs J. / Year: 2019
Title: R180T variant of delta-ornithine aminotransferase associated with gyrate atrophy: biochemical, computational, X-ray and NMR studies provide insight into its catalytic features.
Authors: Montioli, R. / Paiardini, A. / Giardina, G. / Zanzoni, S. / Cutruzzola, F. / Cellini, B. / Borri Voltattorni, C.
History
DepositionOct 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 15, 2020Group: Advisory / Derived calculations / Category: pdbx_unobs_or_zero_occ_atoms / struct_conn
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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: Ornithine aminotransferase, mitochondrial
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6866
Polymers137,9453
Non-polymers7413
Water21,6181200
1
A: Ornithine aminotransferase, mitochondrial
hetero molecules

A: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4584
Polymers91,9632
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,x-y+1,-z+11
2
B: Ornithine aminotransferase, mitochondrial
hetero molecules

B: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4584
Polymers91,9632
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+2/31
3
C: Ornithine aminotransferase, mitochondrial
hetero molecules

C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4584
Polymers91,9632
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Unit cell
Length a, b, c (Å)193.252, 193.252, 57.211
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21A-765-

HOH

31A-826-

HOH

41A-953-

HOH

51B-818-

HOH

61B-880-

HOH

71B-957-

HOH

81B-1000-

HOH

91C-654-

HOH

101C-734-

HOH

111C-793-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 38 - 439 / Label seq-ID: 14 - 415

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.499299, 0.866429, -0.00066), (-0.86643, -0.499299, 0.000822), (0.000382, 0.000982, 0.999999)-96.585899, 55.760311, 9.53673
3given(1), (1), (1)
4given(-0.499487, -0.866315, -0.003167), (0.866309, -0.499496, 0.003408), (-0.004535, -0.001042, 0.999989)0.04461, 111.50779, 19.158501
5given(1), (1), (1)
6given(-0.501118, 0.865379, -0.001003), (-0.865373, -0.501118, -0.003257), (-0.003321, -0.000764, 0.999994)-96.544853, 55.889751, 9.59701

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Components

#1: Protein Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


Mass: 45981.633 Da / Num. of mol.: 3 / Mutation: R180T, A25M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Plasmid: pET43a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 1200 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Prot 115uM in 150mM NaCl 50mM Hepes pH 8.0 mixed with hit 1-5 of the LMB screen (Molecular Dimensions): 4 M Ammonium acetate 0.1 M Bis-Tris propane 7.0 (cryo + Glycerol 20%)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.8→48.31 Å / Num. obs: 110536 / % possible obs: 98.7 % / Redundancy: 8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.049 / Rrim(I) all: 0.145 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8350.39853030.940.1920.44496.2
9.86-48.3110.60.0587190.9990.0190.06298.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.504
Highest resolutionLowest resolution
Rotation47.23 Å1.72 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat


Resolution: 1.8→45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.1649 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.132
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 5358 4.8 %RANDOM
Rwork0.2209 ---
obs0.2212 105147 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.25 Å2 / Biso mean: 15.819 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.19 Å20 Å2
2---0.37 Å20 Å2
3---1.21 Å2
Refinement stepCycle: final / Resolution: 1.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9139 0 45 1200 10384
Biso mean--13.64 26.11 -
Num. residues----1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0199465
X-RAY DIFFRACTIONr_bond_other_d00.028858
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.97912892
X-RAY DIFFRACTIONr_angle_other_deg3.57320482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7951200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97923.929392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.391151531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181553
X-RAY DIFFRACTIONr_chiral_restr0.0670.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110531
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021902
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.71

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A30524.33
2A30482.1
3B30374.65
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 414 -
Rwork0.289 7497 -
all-7911 -
obs--95.98 %

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