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- PDB-6os6: Crystal structure of CymD prenyltransferase complexed with L-tryp... -

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Basic information

Entry
Database: PDB / ID: 6os6
TitleCrystal structure of CymD prenyltransferase complexed with L-tryptophan and DMSPP
ComponentsCymD prenyltransferase
KeywordsTRANSFERASE / prenyltransferase / tryptophan / indole / biosynthesis
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / BENZOIC ACID / DIMETHYLALLYL S-THIOLODIPHOSPHATE / TRYPTOPHAN / Aromatic prenyltransferase, DMATS type
Function and homology information
Biological speciesSalinispora arenicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsRoose, B.W. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD.
Authors: Roose, B.W. / Christianson, D.W.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 2, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8197
Polymers41,0641
Non-polymers7556
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.446, 129.446, 49.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CymD prenyltransferase


Mass: 41064.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora arenicola (strain CNS-205) (bacteria)
Strain: CNS-205 / Gene: Sare_4565 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8M6W6

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Non-polymers , 6 types, 417 molecules

#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1% (w/v) tryptone, 0.05 M HEPES-Na (pH 7.0), 12% PEG 3350
PH range: 7.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.33→29.12 Å / Num. obs: 95021 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 13.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Net I/σ(I): 15 / Num. measured all: 708407
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.33-1.3670.6854765368120.8060.2750.7392.397.3
5.94-29.127.30.041819011230.9980.0160.04444.299.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version ...Starting model: Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing.

5jxm


Resolution: 1.33→29.118 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.8
RfactorNum. reflection% reflection
Rfree0.1809 1993 2.1 %
Rwork0.1662 --
obs0.1665 95019 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.86 Å2 / Biso mean: 18.9029 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: final / Resolution: 1.33→29.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 66 411 3249
Biso mean--15.9 31.36 -
Num. residues----362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3277-1.36090.25011390.2176460659997
1.3609-1.39770.22221430.202366046747100
1.3977-1.43880.2141420.187966226764100
1.4388-1.48520.20311410.178866326773100
1.4852-1.53830.19661420.167366156757100
1.5383-1.59990.16561430.160166276770100
1.5999-1.67270.18141420.159266266768100
1.6727-1.76090.17081450.156166576802100
1.7609-1.87120.16971410.157866286769100
1.8712-2.01560.16911410.162266576798100
2.0156-2.21840.17841400.159166676807100
2.2184-2.53920.18591450.164166736818100
2.5392-3.19850.16531430.172367186861100
3.1985-29.12530.1831460.162868406986100
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)
13.7804-4.5705-3.57046.06024.69974.3018-0.1918-0.2589-0.15970.30480.08040.16770.1884-0.00040.10760.1477-0.00010.01840.12620.03120.12939.6147-1.94634.5718
21.1394-0.00170.03881.23170.43691.35880.013-0.0726-0.02330.0496-0.02140.06560.0279-0.09060.01340.09330.00180.00790.07880.00670.102337.82442.28124.612
34.60140.3389-0.63545.211-0.83182.69360.117-0.02760.0429-0.13110.01010.4058-0.0728-0.2767-0.1080.0862-0.0158-0.03420.1341-0.01210.11625.52336.770614.3803
42.3622-0.2425-2.43441.3202-0.03325.9350.044-0.02620.00330.0042-0.0090.0968-0.1161-0.2066-0.01890.08630.0108-0.0050.0889-0.00050.092933.19029.338419.0601
54.1296-4.8535-0.5726.5742-0.11642.08180.09040.13640.0259-0.2917-0.119-0.0931-0.03860.01950.02840.15630.0189-0.00380.08480.00440.074434.99118.75845.1603
60.6583-0.12950.43021.23280.36570.83260.02360.05410.1164-0.0585-0.0327-0.0531-0.16050.04090.02920.16410.03060.01570.13020.00870.135437.849325.913216.8996
71.2987-0.83311.03331.3939-0.08041.87110.0015-0.11490.1429-0.0573-0.0202-0.1216-0.1521-0.0247-0.01070.1471-0.00140.02340.12350.00410.140143.754427.139824.6648
80.589-0.14630.1340.8930.09230.9329-0.0234-0.06190.02570.05130.0143-0.0599-0.01240.0310.00610.090.00990.00130.1055-0.00380.107648.177314.497331.3817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A2 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 92 )A26 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 120 )A93 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 150 )A121 - 150
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 170 )A151 - 170
6X-RAY DIFFRACTION6chain 'A' and (resid 171 through 231 )A171 - 231
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 270 )A232 - 270
8X-RAY DIFFRACTION8chain 'A' and (resid 271 through 363 )A271 - 363

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