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- PDB-8tn2: Structure of S. hygroscopicus aminotransferase MppQ complexed wit... -

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Basic information

Entry
Database: PDB / ID: 8tn2
TitleStructure of S. hygroscopicus aminotransferase MppQ complexed with pyridoxal-5'-phosphate (PLP)
ComponentsPLP-dependent aminotransferase MppQ
KeywordsBIOSYNTHETIC PROTEIN / MANNOPEPTIMYCIN / AMINOTRANSFERASE / PLP
Function / homologyEnduracididine biosynthesis enzyme MppQ / 2-aminoadipate transaminase activity / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / PLP-dependent aminotransferase MppQ
Function and homology information
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSilvaggi, N.R. / Vuksanovic, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1903899 United States
CitationJournal: Biochemistry / Year: 2023
Title: Structural and Biochemical Characterization of MppQ, an L-Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus.
Authors: Vuksanovic, N. / Melkonian, T.R. / Serrano, D.A. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionAug 1, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionNov 22, 2023ID: 7UKX
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLP-dependent aminotransferase MppQ
B: PLP-dependent aminotransferase MppQ


Theoretical massNumber of molelcules
Total (without water)88,6062
Polymers88,6062
Non-polymers00
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-42 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.730, 114.500, 133.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PLP-dependent aminotransferase MppQ


Mass: 44303.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppQ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q643B9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 15-25 % PEG 3350, and 0.1-0.2 M ammonium citrate trihydrate, trilithium citrate, or ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→41.43 Å / Num. obs: 73140 / % possible obs: 98.3 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Rrim(I) all: 0.132 / Χ2: 0.96 / Net I/σ(I): 10.1 / Num. measured all: 405573
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 94.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.729 / Num. measured all: 20157 / Num. unique obs: 3800 / CC1/2: 0.743 / Rpim(I) all: 0.336 / Rrim(I) all: 0.806 / Χ2: 0.96 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→35.1 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 6815 4.92 %Random
Rwork0.1439 ---
obs0.1452 73087 97.38 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 0 846 6698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076108
X-RAY DIFFRACTIONf_angle_d0.8438332
X-RAY DIFFRACTIONf_dihedral_angle_d12.4492245
X-RAY DIFFRACTIONf_chiral_restr0.05935
X-RAY DIFFRACTIONf_plane_restr0.0121108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.2586750.230612559X-RAY DIFFRACTION93
1.81-1.890.2116660.191612793X-RAY DIFFRACTION94
1.89-1.970.20616590.178512978X-RAY DIFFRACTION96
1.97-2.070.18267150.1613140X-RAY DIFFRACTION97
2.07-2.20.18596190.140613381X-RAY DIFFRACTION99
2.2-2.380.15296750.127913455X-RAY DIFFRACTION99
2.38-2.610.16986790.12513425X-RAY DIFFRACTION99
2.61-2.990.15667570.131713405X-RAY DIFFRACTION99
2.99-3.770.16117050.12713466X-RAY DIFFRACTION100
3.77-35.10.14336650.13713181X-RAY DIFFRACTION97
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)
12.25680.53862.01560.38370.52492.1580.0979-0.0525-0.13850.0404-0.02840.02490.1899-0.0696-0.0770.0966-0.00280.02170.07590.00050.07612.2033-1.768122.4282
20.52580.01640.07770.3918-0.05760.9947-0.0210.12140.0376-0.05320.0111-0.0209-0.02470.06930.00890.0749-0.00160.00070.09780.00940.077925.914914.75217.1245
30.76860.22020.52540.66460.29281.04490.00820.1284-0.0241-0.11860.00650.04370.0399-0.0014-0.01510.09530.00730.0140.1067-0.00340.06814.18732.2334.9512
42-4.221-7.89461.97621.36372-2.3691-5.56743.37812.41011.433-0.4802-2.1584-1.98290.94150.39010.066-0.0720.1912-0.17010.1871-2.5661-4.483-12.1883
50.51660.04870.25790.51980.16750.45190.0092-0.049-0.01080.0514-0.01190.03210.0515-0.0207-0.00390.088-0.00910.02290.0703-0.00270.061816.515611.50634.9472
60.4587-0.23020.0061.48730.44552.0023-0.06180.01680.1483-0.122-0.0101-0.0166-0.16030.07250.05360.1073-0.0282-0.02510.0758-0.0010.150917.534339.377232.0575
70.53110.04640.18371.26510.56450.4516-0.0301-0.05430.11210.0084-0.04710.1561-0.0363-0.05130.06060.0734-0.00190.00750.0828-0.00080.11179.129625.392834.9806
81.861.27030.22472.21190.17871.06480.033-0.22820.26470.23-0.0754-0.0007-0.12340.04560.02020.13550.009-0.00810.1291-0.04240.135227.448325.989551.6757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 402 )
4X-RAY DIFFRACTION4chain 'A' and (resid 403 through 403 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 171 )
7X-RAY DIFFRACTION7chain 'B' and (resid 172 through 298 )
8X-RAY DIFFRACTION8chain 'B' and (resid 299 through 403 )

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