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- PDB-4zm3: Crystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV ... -

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Basic information

Entry
Database: PDB / ID: 4zm3
TitleCrystal structure of PLP-Dependent 3-Aminobenzoate Synthase PctV wild-type
ComponentsAminotransferase
KeywordsTRANSFERASE / Pyridoxal 5-phosphate / Aminotransferase
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesStreptomyces pactum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsHirayama, A. / Miyanaga, A. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology22108003 Japan
CitationJournal: Chembiochem / Year: 2015
Title: Mechanism-Based Trapping of the Quinonoid Intermediate by Using the K276R Mutant of PLP-Dependent 3-Aminobenzoate Synthase PctV in the Biosynthesis of Pactamycin.
Authors: Hirayama, A. / Miyanaga, A. / Kudo, F. / Eguchi, T.
History
DepositionMay 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)200,23912
Polymers198,7824
Non-polymers1,4578
Water6,269348
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8854
Polymers99,3912
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-50 kcal/mol
Surface area26650 Å2
MethodPISA
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3548
Polymers99,3912
Non-polymers9636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-29 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.990, 170.830, 74.570
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA39 - 44359 - 463
21LEULEUBB39 - 44359 - 463
12PROPROAA38 - 44358 - 463
22PROPROCC38 - 44358 - 463
13LEULEUAA39 - 44359 - 463
23LEULEUDD39 - 44359 - 463
14LEULEUBB39 - 44359 - 463
24LEULEUCC39 - 44359 - 463
15LEULEUBB39 - 44359 - 463
25LEULEUDD39 - 44359 - 463
16LEULEUCC39 - 44359 - 463
26LEULEUDD39 - 44359 - 463

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Aminotransferase / Glutamate-1-semialdehyde aminotransferase-like protein


Mass: 49695.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces pactum (bacteria) / Gene: pctV, ptmT / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8R0K5
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 17, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→42.85 Å / Num. obs: 63742 / % possible obs: 95 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.9
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.7 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FQ7

3fq7


Resolution: 2.27→42.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.23 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.43 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22178 3225 5.1 %RANDOM
Rwork0.17983 ---
obs0.18198 60475 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å21.43 Å2
2--1.37 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 2.27→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11738 0 95 348 12181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912051
X-RAY DIFFRACTIONr_bond_other_d0.0080.0211796
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.97516327
X-RAY DIFFRACTIONr_angle_other_deg1.351326915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20551526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15722.162532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.601151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26915135
X-RAY DIFFRACTIONr_chiral_restr0.0890.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113668
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022805
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A230180.09
12B230180.09
21A233770.09
22C233770.09
31A224860.11
32D224860.11
41B228830.09
42C228830.09
51B224030.11
52D224030.11
61C227550.11
62D227550.11
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 210 -
Rwork0.228 4306 -
obs--91.62 %

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