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- PDB-4zm4: Complex structure of PctV K276R mutant with PMP and 3-dehydroshkimate -

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Basic information

Entry
Database: PDB / ID: 4zm4
TitleComplex structure of PctV K276R mutant with PMP and 3-dehydroshkimate
ComponentsAminotransferase
KeywordsTRANSFERASE / pyridoxal 5-phosphate / Aminotransferase
Function / homology
Function and homology information


transaminase activity / biosynthetic process / 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
Chem-P3B / PYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesStreptomyces pactum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
E: Aminotransferase
F: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,80012
Polymers287,0076
Non-polymers1,7936
Water13,818767
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3184
Polymers95,6692
Non-polymers6492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-55 kcal/mol
Surface area26600 Å2
MethodPISA
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1634
Polymers95,6692
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-60 kcal/mol
Surface area26080 Å2
MethodPISA
3
E: Aminotransferase
F: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3184
Polymers95,6692
Non-polymers6492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-53 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.930, 178.930, 467.899
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA10 - 44313 - 446
21LEULEUBB10 - 44313 - 446
12LEULEUAA10 - 44313 - 446
22LEULEUCC10 - 44313 - 446
13GLYGLYAA10 - 43413 - 437
23GLYGLYDD10 - 43413 - 437
14LEULEUAA10 - 44313 - 446
24LEULEUEE10 - 44313 - 446
15LEULEUAA10 - 44313 - 446
25LEULEUFF10 - 44313 - 446
16LEULEUBB10 - 44313 - 446
26LEULEUCC10 - 44313 - 446
17GLYGLYBB10 - 43413 - 437
27GLYGLYDD10 - 43413 - 437
18LEULEUBB10 - 44313 - 446
28LEULEUEE10 - 44313 - 446
19LEULEUBB10 - 44313 - 446
29LEULEUFF10 - 44313 - 446
110GLYGLYCC10 - 43413 - 437
210GLYGLYDD10 - 43413 - 437
111LEULEUCC10 - 44313 - 446
211LEULEUEE10 - 44313 - 446
112LEULEUCC10 - 44313 - 446
212LEULEUFF10 - 44313 - 446
113GLYGLYDD10 - 43413 - 437
213GLYGLYEE10 - 43413 - 437
114GLYGLYDD10 - 43413 - 437
214GLYGLYFF10 - 43413 - 437
115LEULEUEE10 - 44313 - 446
215LEULEUFF10 - 44313 - 446

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 47834.445 Da / Num. of mol.: 6 / Mutation: K276R
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-P3B / (3E,4R,5R)-4,5-dihydroxy-3-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}cyclohex-1-ene-1-carboxylic acid


Mass: 402.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: PEG 4000, magnesium chloride, MES-Na

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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: May 26, 2014
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: 2.4→30 Å / Num. obs: 102961 / % possible obs: 92.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.5 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
MOSFLMdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZM3

4zm3


Resolution: 2.4→29.98 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.022 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.611 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27756 5134 5 %RANDOM
Rwork0.23802 ---
obs0.23999 97822 91.49 %-
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: 31.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.07 Å2-0 Å2
2---0.07 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18832 0 118 767 19717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01919309
X-RAY DIFFRACTIONr_bond_other_d0.0070.0218791
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.97226208
X-RAY DIFFRACTIONr_angle_other_deg1.163342888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18852470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60822.227844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.731153040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.84815212
X-RAY DIFFRACTIONr_chiral_restr0.080.22969
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02122040
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024482
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)
11A259460.05
12B259460.05
21A260740.04
22C260740.04
31A234460.06
32D234460.06
41A259580.05
42E259580.05
51A261250.04
52F261250.04
61B261170.04
62C261170.04
71B234060.06
72D234060.06
81B262660.05
82E262660.05
91B260200.04
92F260200.04
101C234530.05
102D234530.05
111C259370.04
112E259370.04
121C261520.03
122F261520.03
131D234390.06
132E234390.06
141D235020.05
142F235020.05
151E261200.04
152F261200.04
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 401 -
Rwork0.257 7250 -
obs--92.48 %

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