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- PDB-7vrx: Pad-1 in the absence of substrate -

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Basic information

Entry
Database: PDB / ID: 7vrx
TitlePad-1 in the absence of substrate
ComponentsAminotransferase
KeywordsTRANSFERASE / auxin homeostasis / indole-3-pyruvic acid aminotransferase / substrate specificity
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biological speciesSolanum melongena (eggplant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96634676226 Å
AuthorsChoi, M. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning (MSIP) Korea, Republic Of
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Structural and biochemical basis for the substrate specificity of Pad-1, an indole-3-pyruvic acid aminotransferase in auxin homeostasis.
Authors: Choi, M. / Rhee, S.
History
DepositionOct 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Aminotransferase
B: Aminotransferase
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,5398
Polymers180,1554
Non-polymers3844
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-62 kcal/mol
Surface area27290 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-64 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.157, 96.157, 407.132
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUILEILEchain 'A'AA13 - 2213 - 22
12ALAALASERSERchain 'A'AA36 - 23236 - 232
13ALAALALEULEUchain 'A'AA234 - 341234 - 341
14VALVALGLUGLUchain 'A'AA348 - 378348 - 378
21LEULEUILEILEchain 'B'BB13 - 2213 - 22
22ALAALASERSERchain 'B'BB36 - 23236 - 232
23ALAALALEULEUchain 'B'BB234 - 341234 - 341
24VALVALGLUGLUchain 'B'BB348 - 378348 - 378
31LEULEUILEILEchain 'C'CC13 - 2213 - 22
32ALAALASERSERchain 'C'CC36 - 23236 - 232
33ALAALALEULEUchain 'C'CC234 - 341234 - 341
34VALVALGLUGLUchain 'C'CC348 - 378348 - 378
41LEULEUILEILEchain 'D'DD13 - 2213 - 22
42ALAALASERSERchain 'D'DD36 - 23236 - 232
43ALAALALEULEUchain 'D'DD234 - 341234 - 341
44VALVALGLUGLUchain 'D'DD348 - 378348 - 378

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Components

#1: Protein
Aminotransferase


Mass: 45038.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum melongena (eggplant) / Gene: Pad-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J4AG16
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate (pH 4.6), 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 149234 / % possible obs: 99.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 39.1824928583 Å2 / CC1/2: 0.99 / Net I/σ(I): 18.705
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 14983 / CC1/2: 0.396

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000706edata reduction
HKL-2000706edata scaling
PHASER1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O4S

1o4s


Resolution: 1.96634676226→33.8559284365 Å / SU ML: 0.374947785431 / Cross valid method: FREE R-VALUE / σ(F): 1.343541519 / Phase error: 34.7012731992
RfactorNum. reflection% reflection
Rfree0.29055071339 1986 1.33193835258 %
Rwork0.253254153994 147120 -
obs0.253754535002 149106 99.2908084783 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.6478719708 Å2
Refinement stepCycle: LAST / Resolution: 1.96634676226→33.8559284365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11149 0 20 344 11513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061816072910411429
X-RAY DIFFRACTIONf_angle_d1.1104910148315547
X-RAY DIFFRACTIONf_chiral_restr0.044461255871735
X-RAY DIFFRACTIONf_plane_restr0.005607910616161963
X-RAY DIFFRACTIONf_dihedral_angle_d13.19770041684157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96634676226-2.01550.3836340576741400.36805231214110499X-RAY DIFFRACTION99.5043022821
2.0155-2.070.4078752048121460.36057723930710549X-RAY DIFFRACTION100
2.07-2.13090.3510289844961460.35365510056210600X-RAY DIFFRACTION100
2.1309-2.19970.3536742621281460.34953554430910537X-RAY DIFFRACTION100
2.1997-2.27830.424863226871410.34911090872510606X-RAY DIFFRACTION100
2.2783-2.36950.4203839316511420.341724717610553X-RAY DIFFRACTION99.9813031691
2.3695-2.47730.3474140432091430.32550323168510607X-RAY DIFFRACTION99.9906985397
2.4773-2.60780.3608042724661450.30819849129910586X-RAY DIFFRACTION99.9906820723
2.6078-2.77120.2959204721441410.28946741091710592X-RAY DIFFRACTION100
2.7712-2.9850.3289326039931390.27241125950110558X-RAY DIFFRACTION99.9906524584
2.985-3.28520.2890993232511400.25836917869110585X-RAY DIFFRACTION99.99067686
3.2852-3.760.2672235650361420.23429209079310581X-RAY DIFFRACTION99.9627109164
3.76-4.73520.2808403840311400.19428766375110562X-RAY DIFFRACTION99.5349702381
4.7352-33.85592843650.2056998688091350.2070731953749705X-RAY DIFFRACTION91.1955514365

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