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- PDB-7s2x: Structure of SalC, a gamma-lactam-beta-lactone bicyclase for sali... -

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Basic information

Entry
Database: PDB / ID: 7s2x
TitleStructure of SalC, a gamma-lactam-beta-lactone bicyclase for salinosporamide biosynthesis
ComponentsSalC
KeywordsBIOSYNTHETIC PROTEIN / salinosporamide / Marizomib / bicyclase / cyclase / lactam / lactone / ketosynthase / TRANSFERASE
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
RhiE-like, KS-MAT linker domain / : / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Biological speciesSalinispora tropica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChen, P.Y.-T. / Trivella, D.B.B. / Bauman, K.D. / Moore, B.S.
Funding support Brazil, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA127622 Brazil
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI047818 Brazil
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)F31HD101307 Brazil
Sao Paulo Research Foundation (FAPESP)2011/21358-5 Brazil
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Enzymatic assembly of the salinosporamide gamma-lactam-beta-lactone anticancer warhead.
Authors: Bauman, K.D. / Shende, V.V. / Chen, P.Y. / Trivella, D.B.B. / Gulder, T.A.M. / Vellalath, S. / Romo, D. / Moore, B.S.
History
DepositionSep 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SalC
B: SalC
C: SalC
D: SalC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,9219
Polymers259,5264
Non-polymers3955
Water34219
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)84.330, 218.290, 87.870
Angle α, β, γ (deg.)90.000, 111.014, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 11 through 597)
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1(chain "D" and resid 11 through 597)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROTRPA3 - 589
d_21ens_1PROTRPB1 - 587
d_31ens_1PROTRPC1 - 587
d_41ens_1PROTRPD1 - 587

NCS oper:
IDCodeMatrixVector
1given(-0.746211422719, 0.64325143335, -0.171452926765), (0.641212746691, 0.625282769941, -0.444823190826), (-0.178926594125, -0.441869948184, -0.87905416375)30.2026649847, -4.7079357713, 26.6162571051
2given(-0.990454954165, 0.047799258417, 0.129283466321), (0.0200007486275, -0.878179732435, 0.47791246855), (0.136377981447, 0.475936538244, 0.868841445685)-11.7150977263, -114.462579857, 30.0640327422
3given(0.739648451626, -0.672652453662, 0.0214206580086), (-0.670479024316, -0.739260452014, -0.0628638372987), (0.0581209597275, 0.0321350380394, -0.997792209516)-38.5642272476, -95.5928334678, 57.0122366451

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Components

#1: Protein
SalC


Mass: 64881.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora tropica (bacteria) / Gene: salC / Production host: Streptomyces coelicolor (bacteria) / References: UniProt: B0L7F9
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 1.0 uL 1.7-3.4 mg/mL SalC was mixed with 1.0 uL well solution (0.10M HEPES pH 8.5, 30 % (w/v) PEG 3350, and 0.30 M KCl) to make a 2 uL hanging drop in a sealed well with 400 uL well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.85→44.85 Å / Num. obs: 66868 / % possible obs: 96.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 52.17 Å2 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.1 / Net I/σ(I): 11.32
Reflection shellResolution: 2.85→3.02 Å / Num. unique obs: 10562 / CC1/2: 0.698

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 2.85→44.85 Å / SU ML: 0.3529 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.1153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 3312 4.95 %
Rwork0.1974 63534 -
obs0.199 66846 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.21 Å2
Refinement stepCycle: LAST / Resolution: 2.85→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17948 0 19 19 17986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003118376
X-RAY DIFFRACTIONf_angle_d0.600425006
X-RAY DIFFRACTIONf_chiral_restr0.04362710
X-RAY DIFFRACTIONf_plane_restr0.00443341
X-RAY DIFFRACTIONf_dihedral_angle_d20.58746666
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.600580899312
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.786029437044
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.934651315527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.890.35311020.33942275X-RAY DIFFRACTION83.96
2.89-2.930.29191510.29572698X-RAY DIFFRACTION99.1
2.93-2.980.32541420.27952686X-RAY DIFFRACTION99.05
2.98-3.030.28721410.26212735X-RAY DIFFRACTION98.73
3.03-3.080.27741480.26182628X-RAY DIFFRACTION98.79
3.08-3.140.32061330.24732750X-RAY DIFFRACTION98.6
3.14-3.20.25851340.25372634X-RAY DIFFRACTION98.79
3.2-3.260.30021380.25652760X-RAY DIFFRACTION98.91
3.26-3.330.30071530.26292633X-RAY DIFFRACTION98.76
3.33-3.410.28121350.23682689X-RAY DIFFRACTION98.4
3.41-3.50.27841350.22332685X-RAY DIFFRACTION97.58
3.5-3.590.22661320.21042645X-RAY DIFFRACTION98.37
3.59-3.70.1971430.20332694X-RAY DIFFRACTION98.03
3.7-3.820.22831480.19912645X-RAY DIFFRACTION97.42
3.82-3.950.23181350.1962654X-RAY DIFFRACTION97.38
3.95-4.110.21571440.18532668X-RAY DIFFRACTION98.01
4.11-4.30.20481340.16742637X-RAY DIFFRACTION96.89
4.3-4.520.1951360.15662642X-RAY DIFFRACTION96.63
4.52-4.810.20011390.15762660X-RAY DIFFRACTION96.62
4.81-5.180.19451400.17422642X-RAY DIFFRACTION96.4
5.18-5.70.20271380.17872613X-RAY DIFFRACTION95.59
5.7-6.520.22611370.17982646X-RAY DIFFRACTION96.36
6.52-8.20.181410.15042618X-RAY DIFFRACTION95.77
8.21-44.850.1781330.14262597X-RAY DIFFRACTION93.21
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)
11.133975753350.15184500316-0.04419078905991.08204109917-0.1506238863060.7180922112630.077942039143-0.225924792351-0.2078953140990.07817090113970.01245170335250.14475280950.0382812576554-0.152547926781-0.08742433036130.3269469073510.0136099435158-0.01954600273880.3908740449280.05271625678860.357168533589-25.564-70.65743.704
21.09226196241-0.05783676558280.002309685339391.20334903343-0.07713594112190.631712875790.0695054233181-0.10255515759-0.207861453189-0.06672407679240.000446584880548-0.132350419180.1164682250710.0536643981703-0.06613120414590.3447836532490.0267697449487-0.06114592057510.2784928438880.002317235332140.364855990206-3.578-84.60123.998
31.19793475533-0.0407260082415-0.1132665467381.17448376883-0.1434425159970.7611425242260.0268655886587-0.03271185078840.268028972180.02945007105-0.0287435686967-0.422258445544-0.1561983490330.1339609396530.001380219552120.3735771836680.00423404286298-0.0008856640330140.319383038905-0.02485780329970.54071793656315.832-32.230.906
41.252405068510.00651826266847-0.2104616033681.42228270876-0.3841741052171.09769629680.08457427132340.09334448664950.273620496282-0.1801331618040.0267378314933-0.0519039812402-0.217292302256-0.117431915194-0.1002310914340.4265072104870.07896663644540.03670829933380.2680038819070.0128249329360.357852651066-9.01-29.0139.719
51.73583112773-0.2739058818360.07084761098062.38608817922-1.279511075722.911972088890.114314869116-0.549994497004-0.1964239232510.6453926321650.114935244963-0.00205368958034-0.0517741355183-0.216920406725-0.2273097687620.5900035138810.0407055124536-0.08587919419840.5953543202240.06445221152070.337412344267-9.452-76.5772.297
61.757859843790.877627904034-0.1859463946361.929242429770.4374473986361.58619447103-0.1473632629230.286513831859-0.0767903833515-0.4845728791950.1323560189080.1570688984640.1015995651-0.22724713090.006052054369930.4796641322140.0134641376171-0.1252133840340.4208944813550.01037721089090.331008919917-24.39-90.759-1.459
71.2977278427-0.143224824470.0277841684113.361027777211.138579266612.20014921176-0.0710138275321-0.1598308812640.3307960230880.5599566881180.0910156522074-0.188552172675-0.2677216784120.143983322321-0.002490269964060.516099611140.0526483935873-0.0818230152870.337545477982-0.08598293541440.5474924973163.375-12.8655.233
82.402885725240.720212910711-1.454082944631.41121987897-1.396903720913.065754101950.08664989117470.3108657778820.0312327013169-0.110202080177-0.0563884081252-0.067791675379-0.2392525641830.09882257554-0.02300166797680.5347820916780.06100190302820.06443992773230.381159799364-0.001522459923930.4049752722237.296-37.391-18.134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:436 )A9 - 436
2X-RAY DIFFRACTION2( CHAIN B AND RESID 11:436 )B11 - 436
3X-RAY DIFFRACTION3( CHAIN C AND RESID 11:436 )C11 - 436
4X-RAY DIFFRACTION4( CHAIN D AND RESID 11:436 )D11 - 436
5X-RAY DIFFRACTION5( CHAIN A AND RESID 437:597 )A437 - 597
6X-RAY DIFFRACTION6( CHAIN B AND RESID 437:597 )B437 - 597
7X-RAY DIFFRACTION7( CHAIN C AND RESID 437:597 )C437 - 597
8X-RAY DIFFRACTION8( CHAIN D AND RESID 437:597 )D437 - 597

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