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- PDB-8ep7: Crystal Structure of the Ketol-acid Reductoisomerase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 8ep7
TitleCrystal Structure of the Ketol-acid Reductoisomerase from Bacillus anthracis in complex with NADP
ComponentsKetol-acid reductoisomerase (NADP(+)) 2
KeywordsOXIDOREDUCTASE / IlvC / amino acid biosynthesis / Center for Structural Biology of Infectious Diseases / CSBID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ketol-acid reductoisomerase (NADP(+)) 2
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, Y. / Maltseva, N. / Osipiuk, J. / Gu, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) / 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: Crystal Structure of the Ketol-acid Reductoisomerase from Bacillus anthracis in the complex with NADP.
Authors: Kim, Y. / Maltseva, N. / Osipiuk, J. / Gu, M. / Joachimiak, A.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Other / Structure summary / Category: audit_author / pdbx_SG_project
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase (NADP(+)) 2
B: Ketol-acid reductoisomerase (NADP(+)) 2
C: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8208
Polymers112,4333
Non-polymers2,3865
Water3,675204
1
A: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules

A: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4424
Polymers74,9552
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13340 Å2
ΔGint-99 kcal/mol
Surface area23530 Å2
MethodPISA
2
B: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules

B: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5626
Polymers74,9552
Non-polymers1,6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area14340 Å2
ΔGint-103 kcal/mol
Surface area23320 Å2
MethodPISA
3
C: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules

C: Ketol-acid reductoisomerase (NADP(+)) 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6346
Polymers74,9552
Non-polymers1,6794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13920 Å2
ΔGint-110 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.575, 131.860, 132.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-556-

HOH

21C-582-

HOH

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Components

#1: Protein Ketol-acid reductoisomerase (NADP(+)) 2 / KARI 2 / Acetohydroxy-acid isomeroreductase 2 / AHIR 2 / Alpha-keto-beta-hydroxylacyl ...KARI 2 / Acetohydroxy-acid isomeroreductase 2 / AHIR 2 / Alpha-keto-beta-hydroxylacyl reductoisomerase 2 / Ketol-acid reductoisomerase type 1 / Ketol-acid reductoisomerase type I


Mass: 37477.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor / Gene: ilvC2, ilvC-2, BA_1852, GBAA_1852, BAS1716 / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold
References: UniProt: Q81S27, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M lithium acetate, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 56648 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 41.49 Å2 / CC1/2: 0.997 / R split: 0.041 / Rmerge(I) obs: 0.096 / Net I/σ(I): 22.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.191 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2774 / CC1/2: 0.56 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4TSK

4tsk


Resolution: 2.2→41.73 Å / SU ML: 0.3699 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 2795 4.96 %
Rwork0.2167 53552 -
obs0.2191 56347 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7496 0 153 204 7853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00477823
X-RAY DIFFRACTIONf_angle_d0.660810600
X-RAY DIFFRACTIONf_chiral_restr0.04291173
X-RAY DIFFRACTIONf_plane_restr0.0051379
X-RAY DIFFRACTIONf_dihedral_angle_d16.39722846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.39781420.33292542X-RAY DIFFRACTION95.35
2.23-2.280.35171420.30832622X-RAY DIFFRACTION98.96
2.28-2.320.37751300.30042665X-RAY DIFFRACTION99.32
2.32-2.370.32941350.2932655X-RAY DIFFRACTION99.36
2.37-2.420.42731200.29032670X-RAY DIFFRACTION99.22
2.42-2.470.35631170.27712666X-RAY DIFFRACTION99.39
2.47-2.540.33261350.2742659X-RAY DIFFRACTION99.4
2.54-2.60.35221270.28042667X-RAY DIFFRACTION99.47
2.6-2.680.3411240.28012690X-RAY DIFFRACTION99.29
2.68-2.770.36291580.27762653X-RAY DIFFRACTION99.33
2.77-2.870.31481370.28092646X-RAY DIFFRACTION99.29
2.87-2.980.3141510.26482664X-RAY DIFFRACTION99.26
2.98-3.120.31011810.25392633X-RAY DIFFRACTION99.36
3.12-3.280.29681310.22982687X-RAY DIFFRACTION99.65
3.28-3.490.31531390.21992688X-RAY DIFFRACTION99.75
3.49-3.760.23081640.20192701X-RAY DIFFRACTION99.97
3.76-4.130.2262960.18222739X-RAY DIFFRACTION99.79
4.13-4.730.23491450.16242735X-RAY DIFFRACTION99.9
4.73-5.950.21741290.17082762X-RAY DIFFRACTION99.97
5.96-41.730.17771920.17212808X-RAY DIFFRACTION99.34
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)
13.070414356560.3283970266211.218944258967.778779672331.526740642553.73159183034-0.261144361312-0.3972315456480.1463095246852.13038218870.690406054583-0.132911263159-0.1704242425330.59106140383-0.2212521851860.9279363171260.199253306368-0.05344030895520.726760605504-0.2237772252730.53857208700426.578630081912.248904710149.7257931147
23.450647965541.494209576491.14963953757.12662809715-0.2879832169594.870831857240.25628517813-0.462671324076-0.1144104251171.552470506690.3210334387910.04623261878250.1564956373020.184414541256-0.6129220578220.6669217891340.155039304521-0.0244300352550.648492071833-0.1381954684040.526329143525.21705753642.0337701529646.6282930776
34.084991660921.752485921012.233687813950.947946889073-0.6856296463390.12839460480.64280082386-2.309841826390.4009413704290.28785908847-0.2954162104890.05327018038290.0165076726665-0.317271872685-0.008086660413540.504193023134-0.2753970617830.08511369083181.22905556948-0.2211019836260.2624453668171.182548181434.4303541942532.4102805844
45.533329332590.5317801495240.7688725382623.26590371458-1.216230866552.33135322476-0.9595080935321.210004150980.07434255403020.0766223421590.574998550065-0.147742449085-0.9643948518520.7237839928540.3134255302011.02855702861-0.3091491919620.1159199609380.884742836526-0.2223744717490.6488177252527.5561600551447.698676607325.9551727021
52.162210770650.673227283393.012298275310.02143160119020.02788213966182.63872133857-0.36159438586-0.09201138083071.55939966626-0.0180391540375-0.02538956324750.339981534261-0.4759255488720.199531162680.1936053287430.4376030209630.0100632633108-0.07071299606670.273910060937-0.08472564600061.381315389674.4753964170132.3269880941.05629606755
65.257899441362.042714775030.860108432765.379706512141.183716157933.905170117670.17111935154-0.2670720149520.2814094225020.543744586086-0.304050900924-0.416569373586-0.07729405192520.2378657620420.09028743033760.363903212479-0.119471612504-0.03065256110620.387872250875-0.03502687223090.38510383677651.616344373626.531227002910.7358394545
75.056734276042.3744941990.9646077595364.154014412930.9775204250054.37258664546-0.02124530815230.2574788092680.4906702745350.00727404136639-0.02610838788170.000133939590051-0.2257213126970.4389903355730.0478382384150.261555452428-0.0706130833231-0.01197523378660.3372164922070.0107422236080.43528981675245.126236595727.49967241753.3717113316
81.70123430130.1920431403380.1719174062831.749336234920.7055998417990.4337230602170.0713656363712-0.02621322886790.03407101327970.0358346231407-0.0805980932302-0.150361897480.002875776747540.02621530684370.006197320710190.226481704121-0.00986743361801-0.007753055992430.305507283939-0.03758599334980.30170694659530.75886709572.703495789962.97175007012
98.58535451049-5.63693955946-0.6146919735437.238129392083.558757468069.204843193120.175874352652-0.5694693710760.3136734994310.3461221975580.0670953515571-1.518875878070.06825776284890.631520990579-0.3338793043950.493275548085-0.0282743916701-0.1440852149160.4465496062860.00199531363410.58982820313343.6076700506-9.7606545668812.5057135094
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 111 )AA2 - 1111 - 110
22chain 'A' and (resid 112 through 181 )AA112 - 181111 - 176
33chain 'A' and (resid 182 through 323 )AA182 - 323177 - 318
44chain 'B' and (resid 1 through 181 )BC1 - 1811 - 179
55chain 'B' and (resid 182 through 325 )BC182 - 325180 - 323
66chain 'C' and (resid 1 through 91 )CF1 - 911 - 91
77chain 'C' and (resid 92 through 181 )CF92 - 18192 - 181
88chain 'C' and (resid 182 through 309 )CF182 - 309182 - 309
99chain 'C' and (resid 310 through 328 )CF310 - 328310 - 328

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