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- PDB-6v04: DynU16 crystal structure, a putative protein in the dynemicin bio... -

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Basic information

Entry
Database: PDB / ID: 6v04
TitleDynU16 crystal structure, a putative protein in the dynemicin biosynthetic locus
ComponentsUncharacterized SRPBCC domain-containing protein
KeywordsUNKNOWN FUNCTION / dynemicin / START domain / SRPBCC domain / cyclase/aromatase
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily / Uncharacterized conserved protein YndB, AHSA1/START domain
Function and homology information
Biological speciesMicromonospora chersina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsAlvarado, S.K. / Miller, M.D. / Bhardwaj, M. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA217255 United States
National Science Foundation (NSF, United States)STC 1231306 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis.
Authors: Alvarado, S.K. / Miller, M.D. / Bhardwaj, M. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N.
History
DepositionNov 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Sep 15, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 6, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized SRPBCC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0896
Polymers31,9361
Non-polymers1545
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, gel filtration supports monomeric state in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-34 kcal/mol
Surface area12920 Å2
Unit cell
Length a, b, c (Å)73.171, 73.171, 123.944
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-246-

ARG

21A-301-

NA

31A-614-

HOH

41A-629-

HOH

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Components

#1: Protein Uncharacterized SRPBCC domain-containing protein


Mass: 31935.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora chersina (bacteria) / Gene: GA0070603_4194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2BM46
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1ul:1ul, 0.1M Tris-HCl pH8.5, 0.2M MgCl2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.31 Å / Num. obs: 112506 / % possible obs: 95.3 % / Redundancy: 8.974 % / Biso Wilson estimate: 33.908 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.044 / Χ2: 1.162 / Net I/σ(I): 23.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.64.6370.7151.39139930.7990.80673.1
1.6-1.716.8290.4253.07176460.9570.4698.5
1.71-1.8410.4630.2417.47166760.9920.25499.9
1.84-2.0210.4820.11815.28153310.9970.124100
2.02-2.2510.1150.07126.36138730.9990.075100
2.25-2.69.9280.05137.45122510.9990.054100
2.6-3.1810.4020.0452.06103300.9990.04299.9
3.18-4.499.3080.03362.9179930.9990.03599.7
4.49-44.3110.2460.03169.7844130.9990.03399.4

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.25data extraction
PHENIX1.18.2_3874refinement
SHELX2016/1phasing
HKL2Mapphasing
XDSNov 11, 2017data scaling
XDSNov 11, 2017data reduction
xia2data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→34.61 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 2087 3.55 %
Rwork0.1622 56687 -
obs0.1631 58774 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.46 Å2 / Biso mean: 38.6997 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 1.5→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 5 287 2421
Biso mean--30.24 43.98 -
Num. residues----269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542269
X-RAY DIFFRACTIONf_angle_d0.83063108
X-RAY DIFFRACTIONf_chiral_restr0.0528325
X-RAY DIFFRACTIONf_plane_restr0.0055416
X-RAY DIFFRACTIONf_dihedral_angle_d19.0957818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.3284790.27672134221355
1.54-1.580.23011260.23393243336983
1.58-1.620.24261370.21153728386595
1.62-1.670.19341440.19643899404398
1.67-1.720.22631430.18853856399999
1.72-1.780.17251440.17339284072100
1.78-1.850.18731460.17139134059100
1.85-1.940.17951440.161339344078100
1.94-2.040.1761470.153639324079100
2.04-2.170.19011440.152339654109100
2.17-2.340.15381410.148239534094100
2.34-2.570.17381470.16139924139100
2.57-2.940.17471480.160940034151100
2.94-3.710.20351470.156940224169100
3.71-34.610.19121500.1624185433599
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)
10.18350.0316-0.20890.3428-0.05860.26820.2563-0.6630.81720.2885-0.0959-0.2719-0.74370.26980.00170.4571-0.0388-0.01880.43820.02580.405426.429630.707627.1665
20.1173-0.11480.01130.2173-0.01180.05980.5562-0.0085-0.06790.4948-0.1765-0.1094-0.2559-0.8390.00120.39550.1031-0.0130.67760.01170.39049.602229.606221.1735
31.037-0.61130.41090.418-0.28020.1871-0.08190.2317-0.48340.09230.17240.27210.6601-1.57260.07990.2744-0.1241-0.02860.5850.0610.30369.702617.793514.3653
41.05790.3199-0.11260.7895-0.10792.25530.02960.0047-0.2066-0.0241-0.00850.00780.4757-0.2706-0.00010.3082-0.0767-0.03320.23920.00020.268323.139617.618211.0089
50.3145-0.7372-0.18283.9810.92310.2150.2992-0.852-0.30281.43930.03340.45210.7338-1.19160.12270.4366-0.1577-0.02410.53270.1160.408613.84213.46824.2973
61.10360.44130.44051.0405-1.41073.07350.0476-0.4012-0.12870.14830.00410.0980.0624-0.25920.02680.2517-0.0541-0.02690.2450.01760.257923.980721.668219.7359
70.2806-0.3439-0.42311.2787-0.72892.55180.2479-0.08680.53170.2701-0.035-0.1989-0.3887-0.08850.00040.3092-0.02860.00080.28390.0310.268423.812726.987423.6253
80.25320.10480.24120.40170.04840.2370.2651-0.1106-0.1483-0.0261-0.103-0.4344-0.39830.39580.00640.5094-0.1024-0.06940.36430.02740.350629.939735.315719.4737
90.2107-0.04930.08720.0142-0.02770.05-0.33930.11130.1279-0.01930.2019-0.0895-0.6364-0.3209-0.00010.32460.0079-0.0150.38180.03540.278917.955930.85414.1461
100.50970.4492-0.73050.87820.79665.35020.10580.00530.1587-0.28160.14670.6226-0.6909-1.11450.06720.27720.0099-0.03760.65220.04920.29217.405628.34817.6211
110.25020.1448-0.07081.1338-0.27331.38950.0897-0.3662-0.04580.0684-0.0723-0.109-0.0170.017300.2475-0.0223-0.02650.28780.01980.247436.415530.53299.8417
121.13790.25470.8130.53820.4420.7199-0.08330.510.1695-0.168-0.0076-0.5146-0.3550.73080.00020.2575-0.0668-0.00270.43720.03480.363753.227134.11423.5093
131.6894-0.8059-1.48642.3264-0.78582.4494-0.11770.1456-0.324-0.4551-0.02820.02750.2010.10660.00030.3214-0.02820.0060.3163-0.00980.315343.759532.7074-7.3793
142.1738-1.8804-0.51982.78361.39440.89660.11520.20990.7277-0.1553-0.4925-0.3421-0.9220.7593-0.07670.3404-0.14780.0090.31640.01740.32948.736644.02932.6049
152.4769-0.2232-0.93910.82870.62290.86310.11310.00910.24210.0363-0.1212-0.1379-0.38050.1809-0.00020.2583-0.07380.0210.22790.00070.253242.567541.58612.7941
161.32440.9175-0.31680.704-0.82335.37550.0566-0.25240.80470.41940.21360.2408-1.0571-0.54240.18360.3283-0.0567-0.02890.34070.00950.327642.85738.265812.1568
171.51360.7503-0.5673.5703-2.89553.82380.3452-1.133-0.16660.7257-0.14320.564-0.6837-0.15550.14790.3612-0.1492-0.07170.55460.0490.288843.904130.658324.377
180.8870.3555-0.64040.5126-0.58730.7507-0.0477-0.14740.21660.3367-0.155-0.1712-0.52320.0507-0.00540.2895-0.0441-0.01690.24750.00390.246636.630637.21556.9744
191.42850.2942-0.86691.2933-0.09011.06030.11110.2988-0.1447-0.1239-0.02590.08370.0618-0.002500.1995-0.01460.00230.1983-0.01850.20634.534931.0686-1.4471
200.76430.50040.33040.33960.28630.56680.3084-0.3486-2.0590.03350.1099-0.05811.8691-0.25720.04710.4329-0.0281-0.07770.37490.1170.612849.76521.226811.5878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 16 )A10 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 21 )A17 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 35 )A22 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 71 )A36 - 71
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 76 )A72 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 101 )A77 - 101
7X-RAY DIFFRACTION7chain 'A' and (resid 102 through 115 )A102 - 115
8X-RAY DIFFRACTION8chain 'A' and (resid 116 through 123 )A116 - 123
9X-RAY DIFFRACTION9chain 'A' and (resid 124 through 134 )A124 - 134
10X-RAY DIFFRACTION10chain 'A' and (resid 135 through 142 )A135 - 142
11X-RAY DIFFRACTION11chain 'A' and (resid 143 through 164 )A143 - 164
12X-RAY DIFFRACTION12chain 'A' and (resid 165 through 181 )A165 - 181
13X-RAY DIFFRACTION13chain 'A' and (resid 182 through 199 )A182 - 199
14X-RAY DIFFRACTION14chain 'A' and (resid 200 through 204 )A200 - 204
15X-RAY DIFFRACTION15chain 'A' and (resid 205 through 225 )A205 - 225
16X-RAY DIFFRACTION16chain 'A' and (resid 226 through 229 )A226 - 229
17X-RAY DIFFRACTION17chain 'A' and (resid 230 through 234 )A230 - 234
18X-RAY DIFFRACTION18chain 'A' and (resid 235 through 247 )A235 - 247
19X-RAY DIFFRACTION19chain 'A' and (resid 248 through 273 )A248 - 273
20X-RAY DIFFRACTION20chain 'A' and (resid 274 through 278 )A274 - 278

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