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- PDB-6p63: Wild-type NIS synthetase DesD bound to AMP and substrate analog c... -

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Basic information

Entry
Database: PDB / ID: 6p63
TitleWild-type NIS synthetase DesD bound to AMP and substrate analog cadaverine
ComponentsSiderophore Synthetase Type C DesD
KeywordsBIOSYNTHETIC PROTEIN / NIS synthetase / siderophore synthesis
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHoffmann, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1716986 United States
CitationJournal: Biochemistry / Year: 2020
Title: Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family.
Authors: Hoffmann, K.M. / Goncuian, E.S. / Karimi, K.L. / Amendola, C.R. / Mojab, Y. / Wood, K.M. / Prussia, G.A. / Nix, J. / Yamamoto, M. / Lathan, K. / Orion, I.W.
History
DepositionMay 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 23, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / chem_comp / citation / citation_author / diffrn / diffrn_radiation_wavelength / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn.ambient_temp / _diffrn_radiation_wavelength.wavelength / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _software.version / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siderophore Synthetase Type C DesD
B: Siderophore Synthetase Type C DesD
C: Siderophore Synthetase Type C DesD
D: Siderophore Synthetase Type C DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,51516
Polymers266,6614
Non-polymers1,85412
Water16,880937
1
A: Siderophore Synthetase Type C DesD
C: Siderophore Synthetase Type C DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2588
Polymers133,3302
Non-polymers9276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-63 kcal/mol
Surface area42960 Å2
MethodPISA
2
B: Siderophore Synthetase Type C DesD
D: Siderophore Synthetase Type C DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,2588
Polymers133,3302
Non-polymers9276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-59 kcal/mol
Surface area43310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.430, 74.240, 183.170
Angle α, β, γ (deg.)90.000, 94.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Siderophore Synthetase Type C DesD


Mass: 66665.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: CAB87222 / Plasmid: pET44b / Details (production host): C-terminal hexa his tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L069
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.16 M magnesium chloride, 20% PEG, 0.08 M Tris hexahydrate, pH 8.5, 15% glycerol, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryo-cooled / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 16, 2014 / Details: varimax DW
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→89.53 Å / Num. obs: 99262 / % possible obs: 96.2 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.081 / Rrim(I) all: 0.121 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4758 / CC1/2: 0.841 / Rpim(I) all: 0.296 / Rrim(I) all: 0.456 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.22data extraction
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2X0O

2x0o


Resolution: 2.4→69.832 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.164 / Average fsc free: 0.9242 / Average fsc work: 0.9404 / Cross valid method: THROUGHOUT / ESU R: 0.481 / ESU R Free: 0.258
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 4971 5.009 %RANDOM
Rwork0.1681 94263 --
all0.171 ---
obs-99234 95.851 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.251 Å2
Baniso -1Baniso -2Baniso -3
1-0.763 Å2-0 Å2-0.357 Å2
2---0.661 Å2-0 Å2
3----0.042 Å2
Refinement stepCycle: LAST / Resolution: 2.4→69.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18780 0 120 937 19837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01319369
X-RAY DIFFRACTIONr_bond_other_d0.0350.01717745
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.64226371
X-RAY DIFFRACTIONr_angle_other_deg2.4051.5740896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.09652375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52520.8471110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28153046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.25215177
X-RAY DIFFRACTIONr_chiral_restr0.0860.22450
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221956
X-RAY DIFFRACTIONr_gen_planes_other0.0130.024419
X-RAY DIFFRACTIONr_nbd_refined0.210.24035
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.216518
X-RAY DIFFRACTIONr_nbtor_refined0.170.29068
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.28543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2898
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0560.29
X-RAY DIFFRACTIONr_metal_ion_refined0.030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1560.210
X-RAY DIFFRACTIONr_nbd_other0.210.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.210
X-RAY DIFFRACTIONr_mcbond_it0.8181.2129506
X-RAY DIFFRACTIONr_mcbond_other0.8181.2119505
X-RAY DIFFRACTIONr_mcangle_it1.4711.81511876
X-RAY DIFFRACTIONr_mcangle_other1.4711.81511877
X-RAY DIFFRACTIONr_scbond_it0.8131.2779863
X-RAY DIFFRACTIONr_scbond_other0.8131.2789864
X-RAY DIFFRACTIONr_scangle_it1.3881.88214494
X-RAY DIFFRACTIONr_scangle_other1.3881.88214495
X-RAY DIFFRACTIONr_lrange_it3.41913.87721451
X-RAY DIFFRACTIONr_lrange_other3.41913.87921452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.2543570.1916795X-RAY DIFFRACTION93.9693
2.462-2.530.2833520.1926615X-RAY DIFFRACTION94.4294
2.53-2.6030.2463200.1786493X-RAY DIFFRACTION94.5462
2.603-2.6830.2453590.1766298X-RAY DIFFRACTION94.8291
2.683-2.7710.2283060.1676145X-RAY DIFFRACTION95.0214
2.771-2.8680.2483110.1665992X-RAY DIFFRACTION95.3988
2.868-2.9770.2453300.1635743X-RAY DIFFRACTION95.683
2.977-3.0980.2193230.1625517X-RAY DIFFRACTION95.6436
3.098-3.2360.2392650.1555400X-RAY DIFFRACTION96.1963
3.236-3.3940.2192810.1535110X-RAY DIFFRACTION96.1305
3.394-3.5770.222650.164872X-RAY DIFFRACTION96.5965
3.577-3.7940.2092320.1564670X-RAY DIFFRACTION96.8201
3.794-4.0560.1922120.1574411X-RAY DIFFRACTION96.9996
4.056-4.3810.1842070.1514121X-RAY DIFFRACTION97.2147
4.381-4.7990.2042400.1443735X-RAY DIFFRACTION97.5221
4.799-5.3640.2121820.1673470X-RAY DIFFRACTION97.621
5.364-6.1930.3131830.2253042X-RAY DIFFRACTION97.7273
6.193-7.5830.2731090.2192621X-RAY DIFFRACTION98.0956
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)
10.5020.17310.11750.75410.1291.0104-0.0072-0.0830.00890.0941-0.0229-0.07760.00680.10720.03010.05350.0390.00260.12880.01680.09440.2319.613-22.795
20.6684-0.3077-0.29930.63810.14151.09120.0005-0.0189-0.0036-0.0068-0.0013-0.07260.01390.06490.00070.0072-0.0036-0.01750.02050.00390.0682-45.37341.988-68.845
30.7055-0.307-0.2450.70780.14120.9749-0.0161-0.0269-0.01560.00480.0059-0.06140.0110.06750.01010.0092-0.0073-0.01960.03070.00730.06593.8934.489-68.698
40.50080.22140.12350.74150.0851.16250.0192-0.05490.0040.0923-0.02-0.08310.03690.08410.00090.0440.02590.00660.08830.00380.0824-49.24944.346-22.717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 595
2X-RAY DIFFRACTION2ALLB2 - 595
3X-RAY DIFFRACTION3ALLC1 - 595
4X-RAY DIFFRACTION4ALLD2 - 595

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