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- PDB-6os3: Crystal structure of native CymD prenyltransferase -

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Basic information

Entry
Database: PDB / ID: 6os3
TitleCrystal structure of native CymD prenyltransferase
ComponentsCymD prenyltransferase
KeywordsTRANSFERASE / prenyltransferase / tryptophan / indole / biosynthesis
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / alkaloid metabolic process / metal ion binding / Dimethylallyltryptophan synthase CymD
Function and homology information
Biological speciesSalinispora arenicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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: CymD prenyltransferase
B: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8155
Polymers82,1292
Non-polymers6873
Water11,692649
1
A: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4693
Polymers41,0641
Non-polymers4042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3472
Polymers41,0641
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.690, 157.690, 56.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein CymD prenyltransferase


Mass: 41064.328 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 4% 2-propanol, 0.1 M bis-tris propane (pH 9.0), 20% PEG monomethyl ether 5000
PH range: 7.4-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.7→55.75 Å / Num. obs: 76243 / % possible obs: 99.9 % / Redundancy: 15.9 % / Biso Wilson estimate: 16.92 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.06 / Rrim(I) all: 0.24 / Net I/σ(I): 8 / Num. measured all: 1209693 / Scaling rejects: 27
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
1.7-1.73161.1186409540050.7420.2841.1542.9100
9-55.7516.70.11494645680.9930.0290.11819.199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OS6

6os6


Resolution: 1.7→55.75 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.54
RfactorNum. reflection% reflection
Rfree0.2081 1996 2.62 %
Rwork0.1666 --
obs0.1677 76236 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.21 Å2 / Biso mean: 23.6751 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: final / Resolution: 1.7→55.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5245 0 110 649 6004
Biso mean--29.81 32.13 -
Num. residues----694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.74250.26161420.241153035445
1.7425-1.78960.28441390.227652205359
1.7896-1.84230.23151450.213453115456
1.8423-1.90180.21731430.189752435386
1.9018-1.96970.20591440.180352755419
1.9697-2.04860.20931450.170152635408
2.0486-2.14180.21521390.166552955434
2.1418-2.25480.17981470.165753165463
2.2548-2.3960.22411410.163452665407
2.396-2.5810.20731440.170353025446
2.581-2.84080.23681400.172653105450
2.8408-3.25180.21071440.163753255469
3.2518-4.09670.19361430.146153515494
4.0967-55.78180.17891400.145454605600
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)
11.7587-0.3743-0.18520.6658-0.17111.36660.06030.01850.1183-0.03750.0474-0.0541-0.0731-0.0008-0.08450.0938-0.0035-0.00080.0710.00160.1712-28.258523.3263-5.1273
21.2882-0.23980.11240.4122-0.20271.61180.02740.10720.1293-0.1471-0.0219-0.03990.04120.15270.00810.1401-0.01520.00940.09660.00230.1734-10.66422.9091-9.4003
31.63020.12210.34741.80150.49620.99380.0171-0.19010.03120.05140.00020.0281-0.0542-0.0162-0.02040.10990.00110.02770.1151-0.00370.0586-26.700660.4366-21.1808
42.2429-0.0019-0.06422.5724-0.44942.09930.03570.2101-0.0815-0.2401-0.03270.04190.066-0.0341-0.00460.10090.00810.00440.1044-0.01720.0753-26.605151.9794-36.389
52.1044-1.3482-0.93052.24120.8232.04860.09820.26770.0113-0.2624-0.0733-0.0778-0.03070.0566-0.02420.0988-0.00870.00420.1452-0.00580.0853-15.94552.5683-39.5401
62.250.483-0.22360.63410.33681.92010.05280.27120.1834-0.1369-0.0161-0.10230.03110.1125-0.01830.12490.00240.04450.12350.01830.1198-6.470553.2899-37.5609
71.81510.1317-0.95621.365-0.13792.60390.0002-0.22090.03430.08160.0496-0.24670.0010.2443-0.05530.09130.0147-0.01020.1486-0.01320.1251-0.886255.6171-25.0495
82.0581-0.9117-0.23374.33191.32392.2527-0.0439-0.38320.31840.02990.0698-0.40930.07420.2065-0.0470.1476-0.0067-0.010.2439-0.06230.1324-9.397865.8139-10.6681
92.14490.46470.02032.3901-0.07551.9971-0.0225-0.1606-0.01990.05780.058-0.06390.0532-0.029-0.06960.13210.0076-0.00080.1384-0.01820.0819-13.020658.7124-16.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 155 )A5 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 354 )A156 - 354
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 80 )B5 - 80
4X-RAY DIFFRACTION4chain 'B' and (resid 81 through 137 )B81 - 137
5X-RAY DIFFRACTION5chain 'B' and (resid 138 through 172 )B138 - 172
6X-RAY DIFFRACTION6chain 'B' and (resid 173 through 216 )B173 - 216
7X-RAY DIFFRACTION7chain 'B' and (resid 217 through 283 )B217 - 283
8X-RAY DIFFRACTION8chain 'B' and (resid 284 through 312 )B284 - 312
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 348 )B313 - 348

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