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- PDB-2byj: Ornithine aminotransferase mutant Y85I -

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Basic information

Entry
Database: PDB / ID: 2byj
TitleOrnithine aminotransferase mutant Y85I
ComponentsORNITHINE AMINOTRANSFERASE
KeywordsTRANSFERASE / DISEASE MUTATION / TRANSIT PEPTIDE / MITOCHONDRION / PLP-DEPENDENT ENZYME / POLYMORPHISM / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-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 / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsMarkova, M. / Peneff, C. / Hewlins, M.J.E. / Schirmer, T. / John, R.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Determinants of Substrate Specificity in Omega-Aminotransferases.
Authors: Markova, M. / Peneff, C. / Hewlins, M.J.E. / Schirmer, T. / John, R.A.
History
DepositionAug 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3726
Polymers145,6313
Non-polymers7413
Water84747
1
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5824
Polymers97,0872
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-62.5 kcal/mol
Surface area26110 Å2
MethodPISA
2
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5824
Polymers97,0872
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11500 Å2
ΔGint-64.8 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.723, 115.723, 186.551
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-2004-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 36 - 439 / Label seq-ID: 36 - 439

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(-0.4382, -0.87343, 0.21235), (0.78554, -0.48695, -0.38184), (0.43692, -0.00051, 0.8995)71.703, 38.778, 6.707
2given(0.90475, 0.04569, -0.42349), (0.04812, -0.99883, -0.00497), (-0.42322, -0.01588, -0.90589)7.968, 73.86, 43.8

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Components

#1: Protein ORNITHINE AMINOTRANSFERASE


Mass: 48543.652 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 / 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.: 47 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 85 TO ILE ENGINEERED RESIDUE IN CHAIN B, TYR 85 TO ILE ...ENGINEERED RESIDUE IN CHAIN A, TYR 85 TO ILE ENGINEERED RESIDUE IN CHAIN B, TYR 85 TO ILE ENGINEERED RESIDUE IN CHAIN C, TYR 85 TO ILE

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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: 2.78 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.9
Details: 6-10%PEG6000, 120-160MM NACL, 50MM TRICINE PH7.9, 1MM DTT, pH 7.90

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.01→52.7 Å / Num. obs: 28835 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.96
Reflection shellResolution: 3.01→3.16 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.16 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAT

1oat


Resolution: 3.02→29.88 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.875 / SU B: 35.151 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1465 5.1 %RANDOM
Rwork0.207 ---
obs0.208 27299 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å2-0.57 Å20 Å2
2---1.15 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 3.02→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9471 0 45 47 9563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229738
X-RAY DIFFRACTIONr_bond_other_d0.0010.028955
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.97913236
X-RAY DIFFRACTIONr_angle_other_deg0.737320829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83551209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21324.071420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.733151632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5281557
X-RAY DIFFRACTIONr_chiral_restr0.0540.21467
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021920
X-RAY DIFFRACTIONr_nbd_refined0.1890.21930
X-RAY DIFFRACTIONr_nbd_other0.1730.29015
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24761
X-RAY DIFFRACTIONr_nbtor_other0.0830.25042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.246
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.2171
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0581.57848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.0829720
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.14934412
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.2334.53516
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6135 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.010.05
2Btight positional0.010.05
3Ctight positional0.010.05
1Atight thermal0.020.5
2Btight thermal0.020.5
3Ctight thermal0.020.5
LS refinement shellResolution: 3.02→3.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 99
Rwork0.331 1814
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22170.4154-0.39080.64110.05531.6490.0701-0.06170.24530.10320.0333-0.0287-0.45580.3572-0.1034-0.0672-0.0543-0.02990.0245-0.0323-0.086759.992948.845819.6108
21.5864-0.08880.18940.56340.32721.013-0.01750.0925-0.1938-0.05430.0632-0.0720.06260.2494-0.0457-0.1870.0487-0.0053-0.0172-0.0045-0.149256.099727.74120.002
30.831-0.06960.61370.94330.01021.39720.1706-0.0094-0.4134-0.06460.07020.07450.42840.109-0.2408-0.06650.0595-0.0783-0.16010.0350.072618.67675.31185.279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 439
2X-RAY DIFFRACTION2B36 - 439
3X-RAY DIFFRACTION3C36 - 439

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