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- PDB-13bb: Acetolactate synthase large subunit from Mycobacterium gordonae i... -

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Basic information

Entry
Database: PDB / ID: 13bb
TitleAcetolactate synthase large subunit from Mycobacterium gordonae in complex with ThDP
Componentsacetolactate synthase
KeywordsTRANSFERASE / Acetolactate synthase / Structural Genomics / PSI-Biology / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / : / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / acetolactate synthase
Similarity search - Component
Biological speciesMycobacterium gordonae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsTan, K. / Kim, Y. / Pyznarski, T. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Acetolactate synthase from Mycobacterium gordonae in complex with ThDP
Authors: Tan, K. / Kim, Y. / Pyznarski, T. / Endres, M. / Joachimiak, A.
History
DepositionApr 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4456
Polymers59,8091
Non-polymers6365
Water4,990277
1
A: acetolactate synthase
hetero molecules

A: acetolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,89012
Polymers119,6182
Non-polymers1,27210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area10510 Å2
ΔGint-72 kcal/mol
Surface area35010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.006, 156.006, 101.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

21A-782-

HOH

31A-887-

HOH

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Components

#1: Protein acetolactate synthase


Mass: 59809.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium gordonae (bacteria) / Gene: AWC08_14775 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X1X9X3, acetolactate synthase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 MTri HCl pH 8.5, 30 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 3, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.87→78 Å / Num. obs: 51691 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 28.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 2 / Num. unique obs: 3782 / CC1/2: 0.768 / Rpim(I) all: 0.488 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→57.51 Å / SU ML: 0.2368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 2559 4.98 %
Rwork0.1747 48816 -
obs0.1765 51375 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.36 Å2
Refinement stepCycle: LAST / Resolution: 1.87→57.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 39 279 4454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01584311
X-RAY DIFFRACTIONf_angle_d1.37755866
X-RAY DIFFRACTIONf_chiral_restr0.0889661
X-RAY DIFFRACTIONf_plane_restr0.0131784
X-RAY DIFFRACTIONf_dihedral_angle_d16.49941598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.910.35131420.31772652X-RAY DIFFRACTION99.15
1.91-1.950.30731410.27882655X-RAY DIFFRACTION98.73
1.95-1.990.33511350.24892661X-RAY DIFFRACTION98.59
1.99-2.030.26191310.23522674X-RAY DIFFRACTION99.01
2.03-2.080.24931430.21742673X-RAY DIFFRACTION98.7
2.08-2.140.27191510.2062647X-RAY DIFFRACTION99.11
2.14-2.20.2551490.20322688X-RAY DIFFRACTION99.37
2.2-2.280.24041430.19432669X-RAY DIFFRACTION99.26
2.28-2.360.23661590.17822704X-RAY DIFFRACTION99.48
2.36-2.450.23281180.16962693X-RAY DIFFRACTION99.29
2.45-2.560.21691570.16572698X-RAY DIFFRACTION99.69
2.56-2.70.21651410.17122714X-RAY DIFFRACTION99.48
2.7-2.870.22871400.18222713X-RAY DIFFRACTION99.72
2.87-3.090.22181440.18812734X-RAY DIFFRACTION99.86
3.09-3.40.21391280.17682767X-RAY DIFFRACTION99.97
3.4-3.890.18131410.15972763X-RAY DIFFRACTION99.97
3.89-4.90.14471470.13292792X-RAY DIFFRACTION100
4.9-57.510.19711490.15872919X-RAY DIFFRACTION99.9
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)
11.33589951288270.96133890177146-1.89259456860043.6300382808660.805336723633785.07543970105520.0234619691474730.364514014245030.15803664659924-0.373716347268990.0402310984340540.45539142388508-0.25980433628932-0.17315030751393-0.0573878354603640.126652860914010.0029940876999286-0.0760287901745120.295811951105840.0387216767110510.40672412245813-26.8762666688322.9111165887161-13.46416205171
21.4578660965853-0.00840125411697070.147713273452150.94374288831676-0.111343350592731.2612358689082-0.0339885364822890.160206256880270.0054482076008064-0.0110641243410720.0619101368246180.17260981710341-0.033831993962888-0.04386189395941-0.0248988825225290.2105279893666-0.014140034810216-0.0343290885830440.268074273295710.00560487097011590.39668745878245-25.500152316706-5.3047012908605-9.5604528309872
30.941628174874260.264846791754050.945906437645230.414937099420310.283493823687931.91959308334250.0048679731104292-0.0282953718530570.0596177092519390.0574160922366010.0188153542805340.10162642792478-0.187228317910440.022473302492146-0.0297584933232570.21784732361277-0.0221672994259840.01528957011830.20133504570950.00274537159113540.35883281523745-14.273849560556-2.5099476773414-1.0140934723519
40.099023018749444-0.452037360278810.0214292805638192.18187944474780.238271728891811.2727544882081-0.075373331990150.158255685274950.0961120412241640.1124396967565-0.0242522450264010.089522083275793-0.127499819393520.0578712616005550.0895932643310190.18983688326272-0.037416711875026-0.0225759459806790.28216236540710.00336458170256030.34033981698792-14.2064413621484.0334066466612-9.181245045754
51.7804983353636-0.85293244902027-0.690094348134381.7649023586440.698577293783390.78584130473851-0.0879381639008210.42822693706508-0.05771458051584-0.204794042058340.11386461201872-0.0162610114446880.0171788079784760.11879064010872-0.0360390997883410.26655584263751-0.04262046988042-0.0161236510876120.50579243023783-0.0405773703369260.22255627304817-3.9398945894504-6.0224049214685-29.652223723856
61.58379778681540.16475144551994-0.862272797314912.9326427472529-0.39068502620230.49356451995579-0.116869379351630.52180296855093-0.46000692991932-0.259423755174260.232994377678970.100165264540560.14168985786264-0.043323538150445-0.109366090605540.28885321395739-0.039980090478223-0.0285089181876890.57099549151833-0.207918009579010.41715207220791-1.7667345283815-24.697129762057-30.949749295426
71.2088930450758-0.26023108938782-0.305808995267542.299821136368-0.146910224616152.0797834632589-0.0557355670770410.50908722933412-0.36420332176426-0.373094381293070.1540606957618-0.153384749790420.158011142600670.09147227514278-0.0898370527703870.28597172081057-0.0433581643526220.0361484672685440.51306460202299-0.144999793073090.357699276486885.5474698228619-15.913701613137-29.419428414089
83.41581249876770.63849636973993-1.72055381626410.92460464311129-0.0841890093514732.6011899121917-0.259289691003460.44898000012006-1.2615069449745-0.31079454715613-0.00236608232257-0.0700315703503020.42926519303345.1254210277744E-60.286561412817770.42702841283449-0.0067190862500577-0.0276901418703390.46202070754001-0.300114484650540.82345108048054-9.5279783189442-39.630542186569-25.876769746133
91.6913279263098-1.0936561632589-1.47231140017462.05800266716420.625809072830671.3391526777029-0.0344974076132270.33295509913073-0.457661018561-0.0925583476366670.0212692892845080.027503217177710.120739529837080.173982289628810.0100766093012810.27393490156245-0.028597466661155-0.0396601147082760.38304614080793-0.0948735077249310.51264140640953-14.955143105471-24.716118248108-18.891471469971
101.6833677393368-0.14126290568951-0.625083225923991.1510603732899-0.278670042536551.57851241036610.0109180329986150.23189370323879-0.39840893601981-0.0869129848842920.0577517815871110.134756627816410.045550387118795-0.097775836059423-0.0768447884914880.263406551096-0.023958283617919-0.0444323803989130.28990929769656-0.0534598000411780.51607854428444-24.990564067452-24.550793192866-12.56369757837
116.2340135261232-1.7852871838651.09730394113731.9197825172237-0.371088502929482.09462874579840.0484710660584210.18906492553157-0.26522306089352-0.175556374083270.0430306240805390.169839164519110.0763186525727710.051982806202823-0.0783983316598210.283003788568050.010474171630920.00362719966693040.22512050453562-0.0371568761870670.47072522080494-7.4285580100428-36.178607818956-0.92736648166641
123.0934110480954-0.33206718712296-1.59909682041842.36386519380780.455220961928952.5008912284354-0.121212781061640.099379484416-0.86155347479907-0.11120854469551-0.0373619694943520.00669627911480290.308969223061690.247234701006130.174393615903040.341506164982170.015314930447512-0.0622400663368580.30165536246969-0.0562955312531110.68270750643304-18.468883425856-37.555989351542-14.485490073533
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 28 )2 - 281 - 27
22chain 'A' and (resid 29 through 76 )29 - 7628 - 75
33chain 'A' and (resid 77 through 118 )77 - 11876 - 117
44chain 'A' and (resid 119 through 168 )119 - 168118 - 167
55chain 'A' and (resid 169 through 216 )169 - 216168 - 215
66chain 'A' and (resid 217 through 275 )217 - 275216 - 274
77chain 'A' and (resid 276 through 338 )276 - 338275 - 337
88chain 'A' and (resid 339 through 375 )339 - 375338 - 374
99chain 'A' and (resid 376 through 427 )376 - 427375 - 426
1010chain 'A' and (resid 428 through 465 )428 - 465427 - 464
1111chain 'A' and (resid 466 through 492 )466 - 492465 - 491
1212chain 'A' and (resid 493 through 553 )493 - 553492 - 552

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