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- PDB-4wuo: Structure of the E270A Mutant Isopropylmalate dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 4wuo
TitleStructure of the E270A Mutant Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / ISOPROPYLMALATE DEHYDROGENASE / IPMDH / MUTANT
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / identical protein binding / cytosol
Similarity search - Function
Isopropylmalate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / 3-ISOPROPYLMALIC ACID / : / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsPallo, A. / Graczer, E. / Olah, J. / Szimler, T. / Konarev, P.V. / Svergun, D.I. / Merli, A. / Zavodszky, P. / Vas, M. / Weiss, M.S.
Funding support Hungary, 1items
OrganizationGrant numberCountry
NK 108642 Hungary
CitationJournal: Febs Lett. / Year: 2015
Title: Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase.
Authors: Graczer, E. / Pallo, A. / Olah, J. / Szimler, T. / Konarev, P.V. / Svergun, D.I. / Merli, A. / Zavodszky, P. / Weiss, M.S. / Vas, M.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / 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.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 / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,20120
Polymers76,6822
Non-polymers2,51918
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-14 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.180, 143.250, 174.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 27
2112B1 - 27
1122A40 - 74
2122B40 - 74
1132A87 - 107
2132B87 - 107
1142A128 - 141
2142B128 - 141
1152A143 - 147
2152B143 - 147
1162A157 - 192
2162B157 - 192
1172A194 - 224
2172B194 - 224
1182A228 - 305
2182B228 - 305
1192A306 - 311
2192B306 - 311
11102A313 - 346
21102B313 - 346

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.489757, 0.136833, -0.861055), (0.153945, -0.958518, -0.239883), (-0.85816, -0.250039, 0.448376)16.04735, -86.979637, -5.48292
3given(1), (1), (1)
4given(-0.47086, 0.138106, -0.871331), (0.149706, -0.960838, -0.233193), (-0.869413, -0.240245, 0.431744)16.211269, -87.293137, -4.45792
5given(1), (1), (1)
6given(-0.480527, 0.13702, -0.86621), (0.151386, -0.959931, -0.235827), (-0.863815, -0.244453, 0.440529)16.049049, -87.264008, -5.09753
7given(1), (1), (1)
8given(-0.497526, 0.131139, -0.857479), (0.149805, -0.960665, -0.23384), (-0.854416, -0.244796, 0.458311)15.34445, -87.311768, -5.32732
9given(1), (1), (1)
10given(-0.506502, 0.127927, -0.852696), (0.129116, -0.966529, -0.2217), (-0.852516, -0.222388, 0.473032)15.11876, -87.513397, -4.37263
11given(1), (1), (1)
12given(-0.490708, 0.13935, -0.860109), (0.139474, -0.961838, -0.235404), (-0.860089, -0.235477, 0.452546)15.89746, -87.464462, -4.82622
13given(1), (1), (1)
14given(-0.497708, 0.139155, -0.856109), (0.14461, -0.959917, -0.240099), (-0.855205, -0.243301, 0.457635)15.72204, -87.333267, -5.26185
15given(1), (1), (1)
16given(-0.483536, 0.129964, -0.865623), (0.15947, -0.959286, -0.233107), (-0.860676, -0.250756, 0.443124)15.56375, -87.19384, -5.43675
17given(1), (1), (1)
18given(-0.500166, 0.163701, -0.850315), (0.130481, -0.956508, -0.260896), (-0.856042, -0.241442, 0.457053)17.57856, -86.78466, -4.93892
19given(1), (1), (1)
20given(-0.4903, 0.106577, -0.865013), (0.171938, -0.961162, -0.21588), (-0.854426, -0.254575, 0.452933)14.05213, -87.892708, -5.80875

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-isopropylmalate dehydrogenase / 3-IPM-DH / Beta-IPM dehydrogenase / IMDH


Mass: 38340.848 Da / Num. of mol.: 2 / Mutation: E270A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: leuB, TTHA1230 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5SIY4, 3-isopropylmalate dehydrogenase

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Non-polymers , 7 types, 198 molecules

#2: Chemical ChemComp-IPM / 3-ISOPROPYLMALIC ACID


Mass: 176.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O5
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20 % PEG 6000, 10 % ethanol, 0.1 M MOPS-K pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2012
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionHighest resolution: 2.05 Å / Num. obs: 39957 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.093 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.08 / Χ2: 1.02 / Net I/σ(I): 17.23 / Num. measured all: 207793
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.05-2.10.80.6112.7114280293728750.68297.9
2.1-2.160.8670.5033.4715006284628410.55999.8
2.16-2.220.9090.4054.2914643277627740.4599.9
2.22-2.290.9280.3475.1614119270827000.38699.7
2.29-2.370.9480.2915.9513854262326200.32399.9
2.37-2.450.9690.2327.2213287251225110.258100
2.45-2.540.9810.1978.4112909246024540.21999.8
2.54-2.650.9820.1689.7212448235923580.187100
2.65-2.760.990.12912.4911879225322500.14399.9
2.76-2.90.9950.09515.8111476218321820.106100
2.9-3.060.9960.07519.5110846206920680.084100
3.06-3.240.9970.0624.2610274195919560.06699.8
3.24-3.470.9970.0529.559662185318500.05699.8
3.47-3.740.9980.04235.838856171217110.04699.9
3.74-4.10.9990.037408242160316020.04199.9
4.1-4.580.9990.03244.967435145514510.03699.7
4.58-5.290.9990.03146.076567129712930.03499.7
5.29-6.480.9990.03141.795561111311110.03499.8
6.48-9.170.9990.02348.242998718690.02699.8
9.1710.01750.1921505214810.0292.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation36.76 Å3.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MAR345dtbdata collection
XDS11.0.02data reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y41

2y41


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2161 / WRfactor Rwork: 0.1563 / FOM work R set: 0.8195 / SU B: 11.401 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2123 / SU Rfree: 0.1832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2009 5 %RANDOM
Rwork0.1702 37938 --
obs0.1731 -99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 115.26 Å2 / Biso mean: 37.048 Å2 / Biso min: 16.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å2-0 Å20 Å2
2--3.83 Å2-0 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 160 180 5541
Biso mean--34.49 36.3 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195503
X-RAY DIFFRACTIONr_angle_refined_deg1.7262.0167475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9622.884215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29815869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2971548
X-RAY DIFFRACTIONr_chiral_restr0.110.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214144
X-RAY DIFFRACTIONr_mcbond_it3.1273.462784
X-RAY DIFFRACTIONr_mcangle_it4.3826.4583479
X-RAY DIFFRACTIONr_scbond_it4.7833.8762719
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1130TIGHT POSITIONAL0.060.05
184MEDIUM POSITIONAL0.060.5
1108TIGHT THERMAL3.331.5
184MEDIUM THERMAL4.692.5
2100MEDIUM POSITIONAL0.060.5
2139TIGHT THERMAL7.611.5
2100MEDIUM THERMAL8.682.5
381MEDIUM POSITIONAL0.070.5
384TIGHT THERMAL3.041.5
381MEDIUM THERMAL2.932.5
452MEDIUM POSITIONAL0.070.5
456TIGHT THERMAL1.231.5
452MEDIUM THERMAL2.12.5
516MEDIUM POSITIONAL0.10.5
520TIGHT THERMAL4.961.5
516MEDIUM THERMAL3.72.5
6138MEDIUM POSITIONAL0.110.5
6143TIGHT THERMAL1.961.5
6138MEDIUM THERMAL2.962.5
7132MEDIUM POSITIONAL0.080.5
7124TIGHT THERMAL2.011.5
7132MEDIUM THERMAL3.352.5
8230MEDIUM POSITIONAL0.130.5
8312TIGHT THERMAL2.691.5
8230MEDIUM THERMAL3.232.5
925MEDIUM POSITIONAL0.060.5
924TIGHT THERMAL4.351.5
925MEDIUM THERMAL6.792.5
1088MEDIUM POSITIONAL0.060.5
10130TIGHT THERMAL4.921.5
1088MEDIUM THERMAL5.632.5
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 148 -
Rwork0.287 2716 -
all-2864 -
obs--97.98 %
Refinement TLS params.Method: refined / Origin x: -5.7516 Å / Origin y: -47.4987 Å / Origin z: 20.8623 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 345
2X-RAY DIFFRACTION1B1 - 345

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