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- PDB-7q9z: Crystal structure of Chromobacterium violaceum aminotransferase i... -

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Basic information

Entry
Database: PDB / ID: 7q9z
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
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 / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,69112
Polymers109,6642
Non-polymers1,02610
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.150, 60.720, 61.800
Angle α, β, γ (deg.)71.300, 75.940, 85.730
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 33 - 459 / Label seq-ID: 67 - 493

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Probable aminotransferase


Mass: 54832.230 Da / Num. of mol.: 2
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(DE3) (bacteria)
References: UniProt: Q7NWG4, adenosylmethionine-8-amino-7-oxononanoate transaminase

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Non-polymers , 5 types, 86 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.: 2 / Source method: obtained synthetically / Formula: C11H12NO8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v (RS)-2-methyl-2,4-pentanediol (MPD) 0.03M of each of sodium nitrate, disodium hydrogen phosphate and ammonium sulfate in 0.1M MES/imidazole ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v (RS)-2-methyl-2,4-pentanediol (MPD) 0.03M of each of sodium nitrate, disodium hydrogen phosphate and ammonium sulfate in 0.1M MES/imidazole pH6.5 buffer.5 mM PLP and 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: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→56.41 Å / Num. obs: 55363 / % possible obs: 97.8 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 2719 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ah3

4ah3


Resolution: 1.95→56.408 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 15.01 / SU ML: 0.339 / Cross valid method: FREE R-VALUE / ESU R: 0.255 / ESU R Free: 0.202 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2788 2758 4.986 %
Rwork0.2433 52552 -
all0.245 --
obs-55310 97.678 %
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: 64.113 Å2
Baniso -1Baniso -2Baniso -3
1--1.362 Å2-2.605 Å25.517 Å2
2---0.053 Å2-3.352 Å2
3---1.164 Å2
Refinement stepCycle: LAST / Resolution: 1.95→56.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 65 76 6843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126978
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.6379443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66620.891393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.843151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6761558
X-RAY DIFFRACTIONr_chiral_restr0.0880.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025438
X-RAY DIFFRACTIONr_nbd_refined0.2180.23453
X-RAY DIFFRACTIONr_nbtor_refined0.310.24723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2271
X-RAY DIFFRACTIONr_metal_ion_refined0.230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.23
X-RAY DIFFRACTIONr_mcbond_it3.9326.223428
X-RAY DIFFRACTIONr_mcangle_it5.9899.3164285
X-RAY DIFFRACTIONr_scbond_it3.9696.5913550
X-RAY DIFFRACTIONr_scangle_it6.0119.7535151
X-RAY DIFFRACTIONr_lrange_it12.008117.4430428
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.0514239
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.076050.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.076050.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.5752110.56637240.56641630.0660.05994.52320.573
2.001-2.0550.5671720.51138000.51341040.1040.12696.78360.51
2.055-2.1150.5272040.47136130.47439440.2190.23596.77990.458
2.115-2.180.4522110.45135660.45138820.1150.12997.29520.436
2.18-2.2510.4451740.4234700.42237380.2120.21397.48530.397
2.251-2.330.4031720.38333470.38436110.310.33497.45220.358
2.33-2.4180.3831740.36232400.36334930.4490.47197.73830.329
2.418-2.5160.3591850.3330710.33233220.6050.62398.01320.298
2.516-2.6280.3871730.29130030.29632510.7450.77997.6930.259
2.628-2.7560.3051270.26828930.2730730.8210.83398.27530.244
2.756-2.9050.2881460.27427190.27429160.8390.8498.2510.246
2.905-3.080.2941380.24525880.24827660.8370.86998.55390.224
3.08-3.2920.2431100.25924370.25825860.8810.87598.49190.242
3.292-3.5550.29900.2322990.23224300.8890.90698.31280.219
3.555-3.8930.2251220.20320850.20422390.9380.93798.57080.2
3.893-4.350.218890.17619120.17820190.9380.95199.10850.182
4.35-5.0180.1911070.15316400.15617620.9560.96299.14870.163
5.018-6.1340.193980.16114060.16315150.9570.96299.27390.172
6.134-8.6230.185300.14511200.14611590.9520.96899.22350.161
8.623-56.4080.204250.1446190.1466500.9370.96699.07690.169

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