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- PDB-2xr7: Crystal Structure of Nicotiana tabacum malonyltransferase (NtMat1... -

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Basic information

Entry
Database: PDB / ID: 2xr7
TitleCrystal Structure of Nicotiana tabacum malonyltransferase (NtMat1) complexed with malonyl-coa
ComponentsMALONYLTRANSFERASE
KeywordsTRANSFERASE / XENOBIOTICS / NAPHTHOLS
Function / homology
Function and homology information


flavonol-3-O-beta-glucoside O-malonyltransferase / malonyltransferase activity / flavonol-3-O-beta-glucoside O-malonyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / xenobiotic metabolic process / response to toxic substance
Similarity search - Function
: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONYL-COENZYME A / Phenolic glucoside malonyltransferase 1
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsManjasetty, B.A. / Yu, X.H. / Panjikar, S. / Taguchi, G. / Chance, M.R. / Liu, C.J.
CitationJournal: Planta / Year: 2012
Title: Structural Basis for Modification of Flavonol and Naphthol Glucoconjugates by Nicotiana Tabacum Malonyltransferase (Ntmat1).
Authors: Manjasetty, B.A. / Yu, X.H. / Panjikar, S. / Taguchi, G. / Chance, M.R. / Li, C.J.
History
DepositionSep 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Data collection
Revision 1.2Feb 29, 2012Group: Other
Revision 1.3Aug 22, 2012Group: Database references / Refinement description
Revision 1.4Sep 5, 2012Group: Database references
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALONYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2852
Polymers51,4321
Non-polymers8541
Water00
1
A: MALONYLTRANSFERASE
hetero molecules

A: MALONYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5714
Polymers102,8642
Non-polymers1,7072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2020 Å2
ΔGint-17.5 kcal/mol
Surface area38110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.079, 98.079, 151.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein MALONYLTRANSFERASE


Mass: 51431.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) NICOTIANA TABACUM (common tobacco) / Cell: BY-2 / References: UniProt: Q589Y0
#2: Chemical ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
Has protein modificationY
Nonpolymer detailsMALONYL-COA (MLC): PART OF THE LIGAND IS DISORDERED

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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: 3.5 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growDetails: 0.3M AMMONIUM ACETATE, 7% PEG 8K, 10% MPD, PH 5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X29A10.9793
SYNCHROTRONNSLS X3A20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCD
SX-1652CCDOct 25, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1SI(111) MIRRORS
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 25628 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.875 / SU B: 45.734 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1001 7.2 %RANDOM
Rwork0.226 ---
obs0.23 12928 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 82.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 30 0 3574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223670
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9634990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7655451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57223.397156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30515592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8521520
X-RAY DIFFRACTIONr_chiral_restr0.1070.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212774
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.371.52252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8152.53639
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.35851418
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.991101351
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
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 75 -
Rwork0.306 880 -
obs--96.86 %
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)
15.3542-2.6817-1.95373.03881.95731.3223-0.1991-0.3931-0.1010.5548-0.05350.53920.2548-0.11710.25260.53540.02320.09620.46420.14670.4107-15.97-22.58339.884
25.206-1.3056-2.02535.5362.62236.0031-0.1844-0.7377-0.56240.39060.539-0.08480.19250.6465-0.35460.20280.0054-0.04830.28540.16260.3799-4.105-31.48240.045
33.51951.76431.10395.8312-1.73361.6870.0224-0.2882-0.34010.09070.21850.41550.3676-0.3994-0.24090.5707-0.13390.14610.37770.10960.4544-17.314-29.2833.414
45.4107-0.5545-1.40384.00540.65453.84410.1979-0.37010.26930.38250.06070.08370.0193-0.0364-0.25860.212-0.0159-0.0360.36070.14250.1955-10.363-25.86736.8
50.892-0.3457-1.56491.04980.59984.19340.0657-0.0930.23640.42630.0180.254-0.0305-0.4177-0.08380.539-0.00860.01420.59080.06290.5752-18.224-15.11135.731
613.04547.2810.600911.8509-1.51449.9381-0.292-0.21060.5798-0.35370.50280.1921-0.87640.2293-0.21090.1943-0.1383-0.09470.34420.090.241-10.09-3.10710.791
72.9483-0.44811.53943.0327-2.06418.693-0.27430.11550.57330.15380.13840.6441-0.8019-0.60210.13590.31-0.10090.0270.40240.12090.6093-20.412-6.21720.036
80.62490.45220.9810.44421.619921.7546-0.086-0.2141.00680.028-0.08660.7194-2.8882-0.49930.17260.97220.14440.13760.5594-0.06151.8696-20.772.226.037
912.2176-6.99586.64497.7743-5.93685.0951-0.5095-0.51630.7290.12280.31990.0833-0.1556-0.51150.18970.4304-0.1090.01550.50020.01060.4549-13.305-17.84123.667
102.43261.6845-4.1443.39191.167614.4808-0.43570.2847-0.1218-0.37760.7691-0.26410.52010.6592-0.33350.3788-0.0119-0.05780.59790.11920.3948-9.932-17.7679.662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 43
2X-RAY DIFFRACTION2A44 - 79
3X-RAY DIFFRACTION3A80 - 134
4X-RAY DIFFRACTION4A135 - 187
5X-RAY DIFFRACTION5A188 - 247
6X-RAY DIFFRACTION6A248 - 283
7X-RAY DIFFRACTION7A284 - 341
8X-RAY DIFFRACTION8A342 - 370
9X-RAY DIFFRACTION9A371 - 420
10X-RAY DIFFRACTION10A421 - 453

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