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- PDB-8tn3: Structure of S. hygroscopicus aminotransferase MppQ complexed wit... -

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Basic information

Entry
Database: PDB / ID: 8tn3
TitleStructure of S. hygroscopicus aminotransferase MppQ complexed with pyridoxamine 5'-phosphate (PMP)
ComponentsPLP-dependent aminotransferase MppQ
KeywordsBIOSYNTHETIC PROTEIN / MANNOPEPTIMYCIN / AMINOTRANSFERASE / PMP
Function / homology
Function and homology information


2-aminoadipate transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Enduracididine biosynthesis enzyme MppQ / 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
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PLP-dependent aminotransferase MppQ
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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: 7UKY
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,6474
Polymers88,1502
Non-polymers4962
Water12,773709
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-44 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.766, 94.071, 84.287
Angle α, β, γ (deg.)90.00, 95.113, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PLP-dependent aminotransferase MppQ


Mass: 44075.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppQ / Plasmid: pE-SUMOkan / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q643B9
#2: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
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-G / Wavelength: 0.97856 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.63→43.09 Å / Num. obs: 89786 / % possible obs: 97.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.09 / Χ2: 0.96 / Net I/σ(I): 9.91
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3 / Num. unique obs: 8784 / CC1/2: 0.859 / Rpim(I) all: 0.262 / Rrim(I) all: 0.522 / Χ2: 0.96 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→43.07 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 14.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.161 4602 5.11 %Random
Rwork0.1383 ---
obs0.1395 89773 97.09 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 0 32 709 6573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086190
X-RAY DIFFRACTIONf_angle_d1.0028451
X-RAY DIFFRACTIONf_dihedral_angle_d13.3922285
X-RAY DIFFRACTIONf_chiral_restr0.057945
X-RAY DIFFRACTIONf_plane_restr0.0121135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.690.21884260.17768358X-RAY DIFFRACTION95
1.69-1.750.20394830.16618375X-RAY DIFFRACTION96
1.75-1.830.18824560.16278464X-RAY DIFFRACTION96
1.83-1.930.17244340.13998463X-RAY DIFFRACTION97
1.93-2.050.16674840.1328482X-RAY DIFFRACTION97
2.05-2.210.15744860.12918511X-RAY DIFFRACTION97
2.21-2.430.14784460.11938602X-RAY DIFFRACTION98
2.43-2.780.1644610.1328649X-RAY DIFFRACTION98
2.78-3.510.15734540.1418730X-RAY DIFFRACTION99
3.51-43.070.1444720.13748813X-RAY DIFFRACTION99
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)
10.47860.06830.05350.27970.26570.688-0.00120.0057-0.0291-0.0026-0.0192-0.00040.00770.00070.02390.09110.0001-0.00030.06320.01140.12725.6832-5.687542.1698
21.21020.2026-0.35190.6493-0.58451.82970.00370.09960.0079-0.08520.0190.03310.0483-0.02340.03980.08570.0035-0.01680.0411-0.01030.11475.87953.390341.6761
32.6868-0.7663-0.61792.0428-0.26741.85660.03670.426-0.2168-0.2223-0.0819-0.06810.08580.06310.02470.114-0.01170.010.1676-0.02950.113122.981-2.481525.7097
40.8278-0.0314-0.21410.3443-0.12540.973-0.007-0.3147-0.08960.0639-0.0194-0.010.11530.07310.01040.1247-0.0078-0.01660.19350.03510.115912.6147-6.408168.4842
51.6073-0.59630.70251.1365-1.06851.4294-0.012-0.5834-0.04730.1233-0.08-0.17640.05130.210.06690.14440.0081-0.02250.35370.07940.155921.0751-8.642574.2569
61.2817-0.2677-0.22410.8980.07381.4005-0.0889-0.6466-0.09450.27850.11250.07270.0699-0.03540.02360.15820.0249-0.00840.41140.04970.11645.6876-2.167179.6692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 264 )
2X-RAY DIFFRACTION2chain 'A' and (resid 265 through 328 )
3X-RAY DIFFRACTION3chain 'A' and (resid 329 through 403 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 194 )
5X-RAY DIFFRACTION5chain 'B' and (resid 195 through 264 )
6X-RAY DIFFRACTION6chain 'B' and (resid 265 through 403 )

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