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- PDB-4xau: Crystal structure of AtS13 from Actinomadura melliaura -

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Basic information

Entry
Database: PDB / ID: 4xau
TitleCrystal structure of AtS13 from Actinomadura melliaura
ComponentsPutative aminotransferase
KeywordsTRANSFERASE / sugar aminotransferase / Structural Genomics / PSI-2 / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
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
PYRIDOXAL-5'-PHOSPHATE / Putative aminotransferase
Similarity search - Component
Biological speciesActinomadura melliaura (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0012 Å
AuthorsWang, F. / Singh, S. / Xu, W. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01GM098248 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
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 26, 2015Group: Data collection
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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: Putative aminotransferase
B: Putative aminotransferase
C: Putative aminotransferase
D: Putative aminotransferase
E: Putative aminotransferase
F: Putative aminotransferase
G: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,8638
Polymers302,6167
Non-polymers2471
Water4,540252
1
A: Putative aminotransferase
B: Putative aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,4622
Polymers86,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-33 kcal/mol
Surface area27110 Å2
MethodPISA
2
C: Putative aminotransferase
E: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7093
Polymers86,4622
Non-polymers2471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-35 kcal/mol
Surface area26670 Å2
MethodPISA
3
D: Putative aminotransferase
F: Putative aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,4622
Polymers86,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-31 kcal/mol
Surface area27230 Å2
MethodPISA
4
G: Putative aminotransferase

G: Putative aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,4622
Polymers86,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
Buried area4950 Å2
ΔGint-34 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.149, 233.149, 460.859
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21E-406-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYTRPTRPchain AAA-2 - 36918 - 389
2SERSERTRPTRPchain BBB-8 - 36912 - 389
3PROPROPLPPLPchain CCC - H-4 - 50016
4SERSERTRPTRPchain DDD-8 - 36912 - 389
5ARGARGTRPTRPchain EEE-3 - 36917 - 389
6ARGARGTRPTRPchain FFF-3 - 36917 - 389
7ARGARGTRPTRPchain GGG-3 - 36917 - 389

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Components

#1: Protein
Putative aminotransferase


Mass: 43230.875 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura melliaura (bacteria) / Gene: atS13
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q0H2X1
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.98 Å3/Da / Density % sol: 69.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M sodium formate pH 7.0, cryoprotected by adding 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 95972 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 87.6 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.054 / Rrim(I) all: 0.146 / Rsym value: 0.146 / Χ2: 0.616 / Net I/av σ(I): 9.9 / Net I/σ(I): 4.1 / Num. measured all: 975827
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3-3.059.547500.4830.7260.546100
3.05-3.111047880.6170.5570.554100
3.11-3.1710.247100.7550.4610.576100
3.17-3.2310.347850.7540.4070.573100
3.23-3.310.347430.8610.3050.5791000.9320.981
3.3-3.3810.347780.9060.2350.6071000.7180.756
3.38-3.4610.347790.9330.1990.6141000.6070.639
3.46-3.5610.347380.9530.1530.6251000.4670.492
3.56-3.6610.348000.9730.1170.6431000.3580.377
3.66-3.7810.347730.9860.0870.6671000.2650.279
3.78-3.9110.347910.9880.0720.6811000.2190.231
3.91-4.0710.347570.9920.0560.6671000.1720.181
4.07-4.2510.348000.9950.0470.6731000.1420.149
4.25-4.4810.247920.9950.0420.6771000.1270.134
4.48-4.7610.248050.9940.040.6891000.1210.127
4.76-5.1210.248070.9930.0410.7371000.1260.132
5.12-5.6410.248290.9920.0440.7441000.1340.141
5.64-6.4410.248550.9940.0390.5921000.1180.124
6.44-8.0910.148850.9970.0250.4121000.0750.079
8.09-309.850070.9940.0220.45799.90.0660.07

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RXK

4rxk
PDB Unreleased entry


Resolution: 3.0012→29.953 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 1999 2.08 %Random selection
Rwork0.1873 93913 --
obs0.188 95912 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 279.35 Å2 / Biso mean: 109.5 Å2 / Biso min: 30.61 Å2
Refinement stepCycle: final / Resolution: 3.0012→29.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20446 0 16 252 20714
Biso mean--73.16 84.05 -
Num. residues----2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01420938
X-RAY DIFFRACTIONf_angle_d1.19728474
X-RAY DIFFRACTIONf_chiral_restr0.0653137
X-RAY DIFFRACTIONf_plane_restr0.0073728
X-RAY DIFFRACTIONf_dihedral_angle_d12.8887581
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12468X-RAY DIFFRACTION5.248TORSIONAL
12B12468X-RAY DIFFRACTION5.248TORSIONAL
13C12468X-RAY DIFFRACTION5.248TORSIONAL
14D12468X-RAY DIFFRACTION5.248TORSIONAL
15E12468X-RAY DIFFRACTION5.248TORSIONAL
16F12468X-RAY DIFFRACTION5.248TORSIONAL
17G12468X-RAY DIFFRACTION5.248TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0012-3.07620.32061410.31356616675799
3.0762-3.15930.31481430.298366806823100
3.1593-3.25210.31771400.286566216761100
3.2521-3.3570.28751430.256266676810100
3.357-3.47680.25891410.241966656806100
3.4768-3.61580.24041420.223166896831100
3.6158-3.780.22951430.201366946837100
3.78-3.97890.21881420.176266636805100
3.9789-4.22750.20281430.163267096852100
4.2275-4.55290.17641430.154667296872100
4.5529-5.00920.18651430.155867056848100
5.0092-5.72960.2161430.171767376880100
5.7296-7.20210.21261450.18368076952100
7.2021-29.95480.20731470.16356931707899
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)
13.0028-0.44670.20281.44390.27850.795-0.0484-0.12920.01970.31520.0475-0.28990.19350.3053-0.01750.98340.3126-0.09610.8548-0.02480.7525-6.7107-70.9013-68.2104
21.81440.04020.30381.2268-0.12331.5461-0.08850.16680.59290.1027-0.0167-0.163-0.20030.21270.09480.89050.2137-0.03960.720.05410.9285-25.1878-46.3054-82.1924
31.0168-0.22120.12911.59380.26271.80990.10280.07380.2332-0.1092-0.141-0.0592-0.38350.44980.03611.1985-0.0790.13950.9230.0060.6803-34.8286-45.9377-21.8851
42.3077-0.3304-0.55250.95910.08581.5145-0.56080.2777-1.5444-0.2033-0.016-0.36050.72060.05430.54951.4077-0.27520.69511.13-0.23981.83055.1807-92.65423.1329
51.21540.49150.08561.28810.69812.91240.0079-0.1024-0.36210.3285-0.12330.03351.00120.48710.09871.48280.18180.14870.84770.01880.7416-39.1176-79.0943-27.0969
62.48390.7642-0.09961.4436-0.01521.316-0.48720.963-0.5678-0.51980.055-0.27190.23910.04150.40491.2776-0.37010.48781.587-0.25841.284320.8432-72.2266-18.8923
70.2806-0.58240.00930.5439-0.371.0779-0.6773-0.51072.31920.71040.0585-1.4286-0.56780.22290.5291.26620.2056-0.71341.4205-0.30343.244354.4692-61.5864-63.5579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -2 through 369)A0
2X-RAY DIFFRACTION2(chain 'B' and resid -8 through 369)B0
3X-RAY DIFFRACTION3(chain 'C' and resid -4 through 500)C0
4X-RAY DIFFRACTION4(chain 'D' and resid -8 through 369)D0
5X-RAY DIFFRACTION5(chain 'E' and resid -3 through 369)E0
6X-RAY DIFFRACTION6(chain 'F' and resid -3 through 369)F0
7X-RAY DIFFRACTION7(chain 'G' and resid -3 through 369)G0

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