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- PDB-3u1h: Crystal structure of IPMDH from the last common ancestor of Bacillus -

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Basic information

Entry
Database: PDB / ID: 3u1h
TitleCrystal structure of IPMDH from the last common ancestor of Bacillus
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / isocitrate/isopropylmalate dehydrogenase-like fold
Function / homologyIsopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsHaaning, S. / Hobbs, J.K. / Monk, C.R. / Arcus, V.L.
CitationJournal: MOL.BIOL.EVOL. / Year: 2011
Title: On the Origin and Evolution of Thermophily: Reconstruction of Functional Precambrian Enzymes from Ancestors of Bacillus
Authors: Hobbs, J.K. / Shepherd, C. / Saul, D.J. / Demetras, N.J. / Haaning, S. / Monk, C.R. / Daniel, R.M. / Arcus, V.L.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,1872
Polymers85,1872
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-30 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.266, 75.985, 171.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 3 - 364 / Label seq-ID: 24 - 385

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3-isopropylmalate dehydrogenase


Mass: 42593.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: LEUB / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: 3-isopropylmalate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.72 Å3/Da / Density % sol: 54.8 % / Mosaicity: 0.65 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200mM diammonium hydrogen citrate, 2mM MgSO4, 15% PEG 3350, 4% glycerol, pH 5.5, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2010 / Details: msc osmic optics
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→44.549 Å / Num. all: 22393 / Num. obs: 22393 / % possible obs: 95.2 % / Redundancy: 5 % / Rsym value: 0.092 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.954.80.6230.5661.41424029530.2510.6230.5662.487.8
2.95-3.134.80.4280.38821406729250.1740.4280.3883.391.8
3.13-3.354.80.2980.272.81357228230.1230.2980.274.994.2
3.35-3.614.80.1780.1614.71293626940.0740.1780.1618.196
3.61-3.964.80.1340.1215.91228325400.0560.1340.12111.397.5
3.96-4.4350.0930.0848.21154723220.040.0930.08416.598.1
4.43-5.115.30.0720.0659.91096020750.030.0720.06522.498.8
5.11-6.265.60.0670.0610.91008218010.0270.0670.0621.699.5
6.26-8.855.70.0470.04313.5808614270.0190.0470.04329.199.5
8.85-44.5495.30.0410.03713.644028330.0170.0410.03736.598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.61 Å34.65 Å
Translation2.61 Å34.65 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V53

1v53


Resolution: 2.8→44.43 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.013 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 1124 5 %RANDOM
Rwork0.2328 ---
obs0.2367 22331 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.68 Å2 / Biso mean: 65.5073 Å2 / Biso min: 18.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å2-0 Å2
2---0.05 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 0 16 5228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225289
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9957185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70424.821195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.19215865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2351528
X-RAY DIFFRACTIONr_chiral_restr0.1040.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213927
X-RAY DIFFRACTIONr_mcbond_it0.5971.53526
X-RAY DIFFRACTIONr_mcangle_it1.12925599
X-RAY DIFFRACTIONr_scbond_it1.50631763
X-RAY DIFFRACTIONr_scangle_it2.7034.51586
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2574 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.370.5
MEDIUM THERMAL0.512
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 69 -
Rwork0.352 1409 -
all-1478 -
obs--86.99 %

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