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- PDB-6os5: Crystal structure of CymD prenyltransferase complexed with L-tryp... -

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Basic information

Entry
Database: PDB / ID: 6os5
TitleCrystal structure of CymD prenyltransferase complexed with L-tryptophan
ComponentsCymD prenyltransferase
KeywordsTRANSFERASE / prenyltransferase / tryptophan / indole / biosynthesis
Function / homology
Function and homology information


alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups
Similarity search - Function
Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
BENZOIC ACID / DIPHOSPHATE / IMIDAZOLE / TRYPTOPHAN / Aromatic prenyltransferase, DMATS type
Similarity search - Component
Biological speciesSalinispora arenicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 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
C: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1419
Polymers123,1933
Non-polymers9486
Water16,304905
1
A: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3913
Polymers41,0641
Non-polymers3262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5124
Polymers41,0641
Non-polymers4473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CymD prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2382
Polymers41,0641
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.330, 86.330, 141.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein CymD prenyltransferase


Mass: 41064.328 Da / Num. of mol.: 3
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 , 5 types, 911 molecules

#2: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: (0.04 M citric acid, 0.06 M bis-tris propane (pH 6.4)), 20% PEG 3350
PH range: 6.4-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.66→86.33 Å / Num. obs: 123383 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 14.81 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.051 / Rrim(I) all: 0.123 / Net I/σ(I): 8.9 / Num. measured all: 681939 / Scaling rejects: 2968
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
1.66-1.695.60.3983401560560.8860.1840.443.599.7
9.09-86.336.10.18754178820.9570.080.20415.699.3

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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: 1.66→42.665 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.09
RfactorNum. reflection% reflection
Rfree0.1923 2000 1.62 %
Rwork0.1629 --
obs0.1633 123289 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.19 Å2 / Biso mean: 19.5817 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 1.66→42.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7930 0 94 905 8929
Biso mean--17.64 29.69 -
Num. residues----1049
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 (%)
1.66-1.70150.21711410.187585538694100
1.7015-1.74750.20051410.179486048745100
1.7475-1.7990.21511390.170885808719100
1.799-1.8570.20941420.16498547868999
1.857-1.92340.18861460.16488579872599
1.9234-2.00040.20541410.159886338774100
2.0004-2.09140.16891410.154786418782100
2.0914-2.20170.17761450.151886148759100
2.2017-2.33960.20431390.15978631877099
2.3396-2.52030.19161420.16986928834100
2.5203-2.77380.22481450.17688671881699
2.7738-3.17510.20481450.16718709885499
3.1751-3.99980.16841400.155988148954100
3.9998-42.67910.18451530.15699021917499
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)
11.4953-0.3958-0.74311.0525-0.06671.21270.06850.07260.0437-0.0591-0.04250.1011-0.12-0.1558-0.00560.09050.0122-0.01190.0731-0.01670.0727.330948.75532.7017
20.5973-0.0292-0.00620.5763-0.47072.6578-0.0001-0.02430.00120.0801-0.02650.0048-0.0195-0.0390.04230.06530.00940.01330.0781-0.02380.089430.086846.774711.0713
31.3131-0.3214-0.47280.75570.17711.5414-0.0246-0.0453-0.12720.02850.0297-0.07160.1260.2352-0.01280.09270.0043-0.00540.1092-0.00930.095944.028238.761611.5915
41.0776-0.0475-0.04421.69310.15182.20160.00570.05390.0858-0.11590.0796-0.1362-0.17530.2371-0.05920.0924-0.01890.03350.1119-0.01280.099549.051846.2127-5.0597
50.826-0.2879-0.23631.30140.47731.17540.0578-0.02040.14560.06050.0129-0.1666-0.05180.0424-0.05520.067-0.01810.0060.0812-0.00540.122110.876937.200626.9001
62.5266-0.06710.89423.38871.46441.29440.15630.2639-0.0576-0.12140.1084-0.05040.3064-0.058-0.09050.0748-0.0029-0.00160.0791-0.02040.10839.871129.289620.2529
70.87240.199-0.28431.78010.33580.8684-0.0336-0.052-0.0760.05670.02140.05310.12330.0120.00980.09490.0024-0.020.07910.00330.0832.76417.477225.1989
81.0402-0.1861-0.42762.18140.47571.2975-0.0046-0.0473-0.07130.1611-0.03640.20460.0878-0.1340.00750.0697-0.01150.00720.1120.00320.1213-9.267630.408832.8468
93.36620.4016-0.42533.6468-1.17954.114-0.00130.1520.0711-0.11090.01840.14330.2412-0.10530.0140.09460.01190.00890.0932-0.03750.1138-4.534134.370127.7186
100.9858-0.32080.15891.204-0.42891.7006-0.00560.0178-0.1326-0.0294-0.00750.09960.21650.05190.01790.0828-0.00140.00740.0724-0.01190.091732.3033-6.194224.7257
112.0076-0.31560.44292.0999-1.80785.7287-0.03380.05860.0753-0.04310.05010.0199-0.1977-0.12060.08490.05090.0167-0.00560.056-0.00770.083231.66431.308422.1299
122.3446-0.31660.75820.9895-0.48081.5956-0.09710.13640.4118-0.0017-0.0957-0.2138-0.22280.33560.10210.1237-0.0359-0.00550.16290.03650.170542.909513.158620.2798
135.0464-2.9405-0.12944.9705-0.25171.939-0.2157-0.11370.41750.30820.0714-0.1751-0.20540.19110.00750.0981-0.0369-0.03730.13810.01270.122546.41089.683425.1715
141.65460.26110.26572.6460.13541.7763-0.00530.1611-0.069-0.0347-0.0677-0.18430.11390.34630.03770.10250.07320.01420.21320.0280.131551.6185-3.913227.9357
151.40510.0484-0.47842.20640.50831.21260.06730.16890.1186-0.4547-0.08610.11-0.4788-0.21420.00860.22460.0456-0.00370.13310.02110.111831.567354.6738-8.2178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 63 through 120 )C63 - 120
2X-RAY DIFFRACTION2chain 'C' and (resid 121 through 170 )C121 - 170
3X-RAY DIFFRACTION3chain 'C' and (resid 171 through 270 )C171 - 270
4X-RAY DIFFRACTION4chain 'C' and (resid 271 through 347 )C271 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 6 through 120 )A6 - 120
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 138 )A121 - 138
7X-RAY DIFFRACTION7chain 'A' and (resid 139 through 231 )A139 - 231
8X-RAY DIFFRACTION8chain 'A' and (resid 232 through 330 )A232 - 330
9X-RAY DIFFRACTION9chain 'A' and (resid 331 through 358 )A331 - 358
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 120 )B4 - 120
11X-RAY DIFFRACTION11chain 'B' and (resid 121 through 143 )B121 - 143
12X-RAY DIFFRACTION12chain 'B' and (resid 144 through 253 )B144 - 253
13X-RAY DIFFRACTION13chain 'B' and (resid 254 through 283 )B254 - 283
14X-RAY DIFFRACTION14chain 'B' and (resid 284 through 357 )B284 - 357
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 62 )C6 - 62

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