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- PDB-7vo1: Structure of aminotransferase-substrate complex -

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Basic information

Entry
Database: PDB / ID: 7vo1
TitleStructure of aminotransferase-substrate complex
Components454aa long hypothetical 4-aminobutyrate aminotransferase
KeywordsTRANSFERASE / protein-PLP-substrate complex
Function / homology
Function and homology information


ornithine aminotransferase / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PGU / Ornithine aminotransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsSakuraba, H. / Ohshida, T. / Ohshima, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.
Authors: Kawakami, R. / Ohshida, T. / Hayashi, J. / Yoneda, K. / Furumoto, T. / Ohshima, T. / Sakuraba, H.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 454aa long hypothetical 4-aminobutyrate aminotransferase
B: 454aa long hypothetical 4-aminobutyrate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1194
Polymers101,3622
Non-polymers7572
Water52229
1
A: 454aa long hypothetical 4-aminobutyrate aminotransferase
B: 454aa long hypothetical 4-aminobutyrate aminotransferase
hetero molecules

A: 454aa long hypothetical 4-aminobutyrate aminotransferase
B: 454aa long hypothetical 4-aminobutyrate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,2388
Polymers202,7254
Non-polymers1,5134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area27010 Å2
ΔGint-179 kcal/mol
Surface area51420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.740, 113.740, 290.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 454aa long hypothetical 4-aminobutyrate aminotransferase


Mass: 50681.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1423 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50131
#2: Chemical ChemComp-PGU / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid


Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.06 % / Mosaicity: 0.365 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 3000, MgCl2, cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 2, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 23423 / % possible obs: 100 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Rrim(I) all: 0.071 / Χ2: 0.461 / Net I/σ(I): 5.9 / Num. measured all: 438249
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.99-3.0416.20.92411140.9060.2320.9540.43299.9
3.04-3.118.20.88111380.940.210.9060.44100
3.1-3.1619.10.7511490.9510.1750.7710.436100
3.16-3.2219.20.59611350.9650.1380.6120.444100
3.22-3.2919.10.51411400.9790.120.5280.442100
3.29-3.3717.90.42211400.980.1020.4350.462100
3.37-3.45180.36511520.9860.0880.3750.483100
3.45-3.5418.50.29211550.9910.0690.30.483100
3.54-3.6520.30.2811460.9940.0630.2880.536100
3.65-3.7720.40.23311540.9950.0520.2390.747100
3.77-3.920.20.15711540.9970.0350.1610.47100
3.9-4.0619.90.11811640.9980.0270.1210.484100
4.06-4.2419.70.08411540.9990.0190.0860.474100
4.24-4.4719.40.06511670.9990.0150.0670.463100
4.47-4.7518.50.05311870.9990.0130.0550.467100
4.75-5.11170.047118110.0120.0480.45100
5.11-5.6318.80.04411870.9990.010.0450.422100
5.63-6.4419.40.04120610.0090.0410.418100
6.44-8.1118.40.027124510.0060.0280.373100
8.11-5016.40.017135510.0040.0180.27199.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eo5

2eo5


Resolution: 2.99→49.09 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.88 / SU B: 52.281 / SU ML: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 1152 4.9 %RANDOM
Rwork0.2201 ---
obs0.2231 22199 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 199.7 Å2 / Biso mean: 105.239 Å2 / Biso min: 58.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.53 Å20 Å2
2--1.07 Å2-0 Å2
3----3.47 Å2
Refinement stepCycle: final / Resolution: 2.99→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 50 29 7187
Biso mean--107.63 76.96 -
Num. residues----904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137342
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177098
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.6439938
X-RAY DIFFRACTIONr_angle_other_deg1.1971.57816376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7215906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50122.473372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.418151280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3331544
X-RAY DIFFRACTIONr_chiral_restr0.0650.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028252
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021610
LS refinement shellResolution: 2.99→3.068 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 78 -
Rwork0.307 1591 -
all-1669 -
obs--100 %
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)
12.62510.05350.06370.31-0.33440.3893-0.1379-0.54141.1033-0.04920.15070.03990.1265-0.1799-0.01280.33490.1725-0.17470.4993-0.3850.5604-23.8206-38.1655-7.7738
21.17290.01150.09160.1811-0.31650.6085-0.1426-0.10340.1332-0.1080.0906-0.03070.0749-0.10560.0520.3914-0.0106-0.0240.4301-0.17420.0786-12.1821-56.7787-29.1674
31.17480.0136-0.160.1874-0.11790.5361-0.0608-0.26970.5465-0.11620.01580.0524-0.0482-0.04190.04510.33730.0567-0.13420.356-0.26880.3688-8.8109-42.0137-21.1488
40.3322-0.16740.22340.091-0.12780.21110.0776-0.00280.0506-0.01660.0121-0.00120.068-0.08-0.08960.33590.0298-0.06420.52750.01210.2729-44.7474-47.0385-32.1424
50.94770.1670.26420.45790.12350.1275-0.2079-0.34170.1127-0.03510.1566-0.05980.0509-0.13240.05130.3827-0.01980.04290.6488-0.2280.0838-32.4333-69.8231-16.2183
61.1512-0.7057-0.42971.5416-0.38331.0176-0.1351-0.27740.1372-0.19960.02390.11140.2565-0.3490.11120.32250.02470.0180.6974-0.36670.2229-41.0699-69.1532-12.0031
70.7839-0.75480.20191.2043-0.64220.4849-0.1591-0.18730.167-0.09710.29460.02910.1636-0.2105-0.13540.2617-0.0567-0.09780.7149-0.13740.1504-50.1715-62.0883-25.3009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 86
2X-RAY DIFFRACTION2A87 - 228
3X-RAY DIFFRACTION3A229 - 454
4X-RAY DIFFRACTION4B3 - 85
5X-RAY DIFFRACTION5B86 - 234
6X-RAY DIFFRACTION6B235 - 295
7X-RAY DIFFRACTION7B296 - 454

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