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- PDB-7q9x: Crystal structure of Chromobacterium violaceum aminotransferase i... -

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Basic information

Entry
Database: PDB / ID: 7q9x
TitleCrystal structure of Chromobacterium violaceum aminotransferase in complex with PLP-pyruvate adduct
ComponentsProbable aminotransferase
KeywordsTRANSFERASE / Transaminase / inhibition / pyridoxal phosphate
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
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-AN7 / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIsupov, M.N. / Mitchell, D. / Sayer, C. / Littlechild, J.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/T002875/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L002035/1 United Kingdom
CitationJournal: To Be Published
Title: Aminotransferase from Chromobacterium violaceum in complex with PLP-pyruvate adduct.
Authors: Isupov, M.N. / Mitchell, D. / Sayer, C. / Littlechild, J.A.
History
DepositionNov 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
AAA: Probable aminotransferase
BBB: Probable aminotransferase
CCC: Probable aminotransferase
DDD: Probable aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,22194
Polymers219,3294
Non-polymers3,89390
Water36,5882031
1
AAA: Probable aminotransferase
BBB: Probable aminotransferase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 112 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)111,72448
Polymers109,6642
Non-polymers2,05946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CCC: Probable aminotransferase
DDD: Probable aminotransferase
hetero molecules


  • defined by author
  • 111 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)111,49846
Polymers109,6642
Non-polymers1,83344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.330, 61.380, 116.480
Angle α, β, γ (deg.)103.560, 89.380, 105.420
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 5 - 459 / Label seq-ID: 39 - 493

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
211BBBB
322AAAA
422CCCC
533AAAA
633DDDD
744BBBB
844CCCC
955BBBB
1055DDDD
1166CCCC
1266DDDD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Probable aminotransferase


Mass: 54832.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: CV_2025 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q7NWG4, adenosylmethionine-8-amino-7-oxononanoate transaminase

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Non-polymers , 7 types, 2121 molecules

#2: Chemical
ChemComp-AN7 / (3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid


Mass: 317.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12NO8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 77 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2031 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 290 K / Method: microbatch
Details: 12.5% PEG 8000 and 50 mM HEPES pH 7.5 10 mM PLP, 5 mM pyruvate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→39.43 Å / Num. obs: 156999 / % possible obs: 76.1 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 14.9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3529 / CC1/2: 0.861 / % possible all: 23

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ba4

4ba4


Resolution: 1.6→39.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.158 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2612 7878 5.018 %
Rwork0.2273 149118 -
all0.229 --
obs-156996 76.103 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.71 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14296 0 213 2031 16540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01215572
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.63821238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89452037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10221.099901
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.417152598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.68515131
X-RAY DIFFRACTIONr_chiral_restr0.060.21924
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212265
X-RAY DIFFRACTIONr_nbd_refined0.2110.28550
X-RAY DIFFRACTIONr_nbtor_refined0.2990.210435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.21926
X-RAY DIFFRACTIONr_metal_ion_refined0.290.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3260.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.2106
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2250.22
X-RAY DIFFRACTIONr_mcbond_it1.013.9897516
X-RAY DIFFRACTIONr_mcangle_it1.6676.7129450
X-RAY DIFFRACTIONr_scbond_it1.2544.4888056
X-RAY DIFFRACTIONr_scangle_it2.0437.38811678
X-RAY DIFFRACTIONr_lrange_it6.76724.1826573
X-RAY DIFFRACTIONr_ncsr_local_group_10.0710.0515789
X-RAY DIFFRACTIONr_ncsr_local_group_20.0570.0515972
X-RAY DIFFRACTIONr_ncsr_local_group_30.070.0515794
X-RAY DIFFRACTIONr_ncsr_local_group_40.0780.0515835
X-RAY DIFFRACTIONr_ncsr_local_group_50.0660.0515991
X-RAY DIFFRACTIONr_ncsr_local_group_60.0710.0515899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.070590.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.070590.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.056740.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.056740.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.070470.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.070470.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.077930.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.077930.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.066260.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.066260.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.070510.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.070510.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.3461720.3673354X-RAY DIFFRACTION23.0397
1.642-1.6870.3562080.3584272X-RAY DIFFRACTION30.2539
1.687-1.7360.3422750.3395290X-RAY DIFFRACTION38.3793
1.736-1.7890.3173340.3186411X-RAY DIFFRACTION48.0071
1.789-1.8480.3434350.3267822X-RAY DIFFRACTION60.584
1.848-1.9120.3675170.30510230X-RAY DIFFRACTION81.8632
1.912-1.9840.2996150.28211629X-RAY DIFFRACTION96.2125
1.984-2.0650.2855580.26311211X-RAY DIFFRACTION96.5226
2.065-2.1570.2955420.23910836X-RAY DIFFRACTION96.8505
2.157-2.2620.2695540.23310298X-RAY DIFFRACTION97.1444
2.262-2.3840.2645350.2279862X-RAY DIFFRACTION97.3137
2.384-2.5290.264890.2179345X-RAY DIFFRACTION97.5789
2.529-2.7030.2734780.2158759X-RAY DIFFRACTION97.6737
2.703-2.9190.2544450.2048216X-RAY DIFFRACTION97.8202
2.919-3.1970.2473970.1937560X-RAY DIFFRACTION98.1497
3.197-3.5730.2083900.1826807X-RAY DIFFRACTION98.2123
3.573-4.1230.2273270.1816017X-RAY DIFFRACTION98.1587
4.123-5.0430.2112780.1875098X-RAY DIFFRACTION97.9592
5.043-7.1050.2272310.2123930X-RAY DIFFRACTION98.8596
7.105-39.430.228980.2382171X-RAY DIFFRACTION95.8193

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