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- PDB-4zwv: Crystal Structure of Aminotransferase AtmS13 from Actinomadura me... -

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Basic information

Entry
Database: PDB / ID: 4zwv
TitleCrystal Structure of Aminotransferase AtmS13 from Actinomadura melliaura
ComponentsPutative aminotransferase
KeywordsTRANSFERASE / aminotransferase / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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 ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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
Putative aminotransferase
Similarity search - Component
Biological speciesActinomadura melliaura (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.503 Å
AuthorsKim, Y. / Bigelow, L. / Endres, M. / Wang, F. / Phillips Jr., G.N. / Joachimiak, A. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA84374 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: Proteins / Year: 2015
Title: Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis.
Authors: Singh, S. / Kim, Y. / Wang, F. / Bigelow, L. / Endres, M. / Kharel, M.K. / Babnigg, G. / Bingman, C.A. / Joachimiak, A. / Thorson, J.S. / Phillips, G.N.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionJun 3, 2015ID: 4RXK
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Structure summary
Revision 1.3Jul 29, 2015Group: Database references
Revision 1.4Oct 14, 2015Group: Data collection
Revision 2.0Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Non-polymer description / Structure summary
Category: entity / pdbx_audit_support / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aminotransferase
B: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2386
Polymers83,8702
Non-polymers3684
Water20,8071155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-33 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.137, 73.025, 58.607
Angle α, β, γ (deg.)90.000, 103.680, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0 - 369
211chain BB0 - 369

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Components

#1: Protein Putative aminotransferase


Mass: 41935.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura melliaura (bacteria) / Gene: atS13 / Plasmid: PMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0H2X1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride, 20 % (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 250365 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 13.79 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.052 / Χ2: 2.561 / Net I/σ(I): 14.85 / Num. measured all: 560589
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.590.8190.32136102942331342180.42980.8
1.59-1.70.9130.2334.968686739821391890.30298.4
1.7-1.840.9710.1338.278558937075368350.17199.4
1.84-2.020.990.07512.857908834090338470.09799.3
2.02-2.250.9950.04718.197159130818305030.06199
2.25-2.60.9970.03623.066286927240268540.04698.6
2.6-3.180.9970.02927.575235623007224460.03897.6
3.18-4.490.9980.02332.93965817758171960.0396.8
4.490.9980.02334.7521542983792770.03194.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
SHELXDEphasing
HKL-3000phasing
RefinementResolution: 1.503→49.586 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1667 12571 5.02 %
Rwork0.1457 237771 -
obs0.1468 250342 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.27 Å2 / Biso mean: 19.7321 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: final / Resolution: 1.503→49.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 24 1155 6997
Biso mean--33.98 35.39 -
Num. residues----740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066475
X-RAY DIFFRACTIONf_angle_d1.1048870
X-RAY DIFFRACTIONf_chiral_restr0.045952
X-RAY DIFFRACTIONf_plane_restr0.0061181
X-RAY DIFFRACTIONf_dihedral_angle_d13.2342414
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3290X-RAY DIFFRACTION3.068TORSIONAL
12B3290X-RAY DIFFRACTION3.068TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5029-1.51990.24072890.23635540582968
1.5199-1.53780.25833250.22426338666376
1.5378-1.55660.23093760.21166764714082
1.5566-1.57630.21823740.20657233760787
1.5763-1.5970.20744320.20337762819493
1.597-1.61890.23354400.19368016845696
1.6189-1.6420.22244600.19398069852998
1.642-1.66650.22244300.184682528682100
1.6665-1.69260.18514430.172482508693100
1.6926-1.72030.17175040.164281848688100
1.7203-1.750.19294100.15738243865399
1.75-1.78180.18353940.14838358875299
1.7818-1.81610.1674400.15138116855699
1.8161-1.85320.18064230.14728301872499
1.8532-1.89350.17154260.1488279870599
1.8935-1.93750.16984350.14888176861199
1.9375-1.9860.14194610.14338238869999
1.986-2.03970.18394000.14268273867399
2.0397-2.09970.15484340.13828246868099
2.0997-2.16750.16324440.14268214865899
2.1675-2.24490.16794040.14058148855299
2.2449-2.33480.16684250.13738242866799
2.3348-2.44110.15513830.13918230861398
2.4411-2.56980.16324250.14438185861099
2.5698-2.73070.15224250.14068095852098
2.7307-2.94160.18044250.14668152857798
2.9416-3.23750.16134160.1428083849998
3.2375-3.70590.14554770.12847986846397
3.7059-4.66850.13614560.11577966842297
4.6685-49.61290.16293950.1427832822794
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)
10.5766-0.0053-0.02060.7330.22790.6120.0175-0.05630.1140.0467-0.0430.0756-0.0421-0.05680.01730.0841-0.0091-0.00490.079-0.00420.101524.43670.499512.7621
20.6827-0.0382-0.22540.80580.21780.5746-0.01920.0591-0.0710.0088-0.01630.00620.075-0.04080.02850.079-0.0077-0.00550.07510.00510.076327.185438.66973.3028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 369)A0
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 369)B0

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