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- PDB-5e4r: Crystal structure of domain-duplicated synthetic class II ketol-a... -

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Basic information

Entry
Database: PDB / ID: 5e4r
TitleCrystal structure of domain-duplicated synthetic class II ketol-acid reductoisomerase 2Ia_KARI-DD
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / ketol-acid reductiosomerase / protein knot / psuedodimer / protein engineering / chimera protein
Function / homology
Function and homology information


ketol-acid reductoisomerase [NAD(P)+] / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Acetohydroxy acid isomeroreductase, catalytic 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
oxo(propan-2-ylamino)acetic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ketol-acid reductoisomerase (NAD(P)(+))
Similarity search - Component
Biological speciesIgnisphaera aggregans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsCahn, J.K.B. / Brinkmann-Chen, S. / Buller, A.R. / Arnold, F.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Gordon and Betty Moore FoundationGBMF2809 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Artificial domain duplication replicates evolutionary history of ketol-acid reductoisomerases.
Authors: Cahn, J.K. / Brinkmann-Chen, S. / Buller, A.R. / Arnold, F.H.
History
DepositionOct 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3397
Polymers55,2621
Non-polymers1,0776
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.882, 103.882, 142.074
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-824-

HOH

21A-835-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ketol-acid reductoisomerase / Acetohydroxy-acid isomeroreductase / Alpha-keto-beta-hydroxylacyl reductoisomerase


Mass: 55261.930 Da / Num. of mol.: 1 / Fragment: UNP residues 1-335,189-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1) (archaea)
Strain: DSM 17230 / JCM 13409 / AQ1.S1 / Gene: ilvC, Igag_1561 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E0SRA9, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 6 types, 243 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-40E / oxo(propan-2-ylamino)acetic acid


Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe molecule is a chimera composed of ~1.5 copies of the I. aggregans KARI, so the 145 residues at ...The molecule is a chimera composed of ~1.5 copies of the I. aggregans KARI, so the 145 residues at the C-terminal are also from that protein (and match the 145 residues before them).

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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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2015
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.922→103.882 Å / Num. obs: 59315 / % possible obs: 99.2 % / Redundancy: 10.3 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.085 / Rsym value: 0.081 / Net I/av σ(I): 8.067 / Net I/σ(I): 19.2 / Num. measured all: 613837
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.92-2.038.20.6081.36598080800.2220.6083.494.4
2.03-2.15110.38328975681480.120.3836.4100
2.15-2.310.70.2433.28177276760.0770.2439.4100
2.3-2.4810.80.1764.47730971610.0560.17612.3100
2.48-2.7210.90.12867187566220.0410.12816.2100
2.72-3.0410.50.0888.56320360110.0280.08822.3100
3.04-3.5110.90.05812.35799853370.0180.05833.5100
3.51-4.310.50.04315.84810345690.0140.04345.1100
4.3-6.0810.30.03816.53707736000.0120.03847.2100
6.08-38.8819.80.0318.72076421110.010.0348.199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.78 Å38.88 Å
Translation6.78 Å38.88 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
SCALA3.3.21data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XDZ

4xdz


Resolution: 1.94→103.88 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1707 / WRfactor Rwork: 0.1491 / FOM work R set: 0.8941 / SU B: 4.206 / SU ML: 0.062 / SU R Cruickshank DPI: 0.1003 / SU Rfree: 0.0959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 2862 4.9 %RANDOM
Rwork0.1577 ---
obs0.1587 55302 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.1 Å2 / Biso mean: 29.162 Å2 / Biso min: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.94→103.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 69 238 3924
Biso mean--25.5 36.99 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193893
X-RAY DIFFRACTIONr_bond_other_d0.0010.023794
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9955261
X-RAY DIFFRACTIONr_angle_other_deg0.64738732
X-RAY DIFFRACTIONr_chiral_restr0.0910.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024312
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02847
X-RAY DIFFRACTIONr_mcbond_it2.5822.0461928
X-RAY DIFFRACTIONr_mcbond_other2.5772.0431927
X-RAY DIFFRACTIONr_mcangle_it3.3713.0412412
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 232 -
Rwork0.218 4000 -
all-4232 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: 22.9951 Å / Origin y: 45.565 Å / Origin z: -0.8893 Å
111213212223313233
T0.0241 Å2-0.0199 Å20.012 Å2-0.0573 Å20.0124 Å2--0.0249 Å2
L0.2727 °2-0.0834 °2-0.2133 °2-0.1867 °2-0.1598 °2--0.5904 °2
S0.0547 Å °-0.0264 Å °0.0663 Å °-0.0512 Å °0.0035 Å °-0.0375 Å °0.0226 Å °-0.0549 Å °-0.0582 Å °

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