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- PDB-4xdy: Structure of NADH-preferring ketol-acid reductoisomerase from an ... -

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Basic information

Entry
Database: PDB / ID: 4xdy
TitleStructure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


ketol-acid reductoisomerase (NAD+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding
Similarity search - Function
ProC C-terminal domain-like fold / ProC C-terminal domain-like fold - #10 / 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. ...ProC C-terminal domain-like fold / ProC C-terminal domain-like fold - #10 / 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 / Helix non-globular / Special / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-HYDROXY-N-ISOPROPYLOXAMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Ketol-acid reductoisomerase (NAD(+))
Similarity search - Component
Biological speciesuncultured archaeon GZfos26G2 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.535 Å
AuthorsCahn, J.K.B. / Brinkmann-Chen, S. / Arnold, F.H.
Citation
Journal: Biochem.J. / Year: 2015
Title: Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases.
Authors: Cahn, J.K. / Brinkmann-Chen, S. / Spatzal, T. / Wiig, J.A. / Buller, A.R. / Einsle, O. / Hu, Y. / Ribbe, M.W. / Arnold, F.H.
#1: Journal: Metab. Eng. / Year: 2014
Title: Uncovering rare NADH-preferring ketol-acid reductoisomerases.
Authors: Brinkmann-Chen, S. / Cahn, J.K. / Arnold, F.H.
History
DepositionDec 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Data collection
Revision 1.2Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase
B: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,41514
Polymers75,4602
Non-polymers1,95512
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16550 Å2
ΔGint-184 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.695, 141.748, 148.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 37730.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured archaeon GZfos26G2 (environmental samples)
Gene: ilvC, GZ26G2_30 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3)
References: UniProt: Q64BR7, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 5 types, 371 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Mg
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-HIO / N-HYDROXY-N-ISOPROPYLOXAMIC ACID


Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M bis-tris pH 5, 20% w/v polyethylene glycol 1500

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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: Mar 30, 2013
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: 1.535→102.57 Å / Num. obs: 157419 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rsym value: 0.088 / Net I/σ(I): 7.2
Reflection shellResolution: 1.535→1.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KQX

4kqx


Resolution: 1.535→102.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.989 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20914 7699 5 %RANDOM
Rwork0.17875 ---
obs0.18022 145320 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.535→102.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 126 359 5629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195537
X-RAY DIFFRACTIONr_bond_other_d0.0010.025281
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9897502
X-RAY DIFFRACTIONr_angle_other_deg0.95312229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1280.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021189
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2462.3332725
X-RAY DIFFRACTIONr_mcbond_other2.2452.332724
X-RAY DIFFRACTIONr_mcangle_it2.923.4843429
X-RAY DIFFRACTIONr_mcangle_other2.9243.4863430
X-RAY DIFFRACTIONr_scbond_it3.6632.6792812
X-RAY DIFFRACTIONr_scbond_other3.6632.6792812
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3493.864074
X-RAY DIFFRACTIONr_long_range_B_refined6.04124.2545057
X-RAY DIFFRACTIONr_long_range_B_other6.04124.2585058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.535→1.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 432 -
Rwork0.391 7821 -
obs--71.75 %

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