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- PDB-3udu: Crystal structure of putative 3-isopropylmalate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 3udu
TitleCrystal structure of putative 3-isopropylmalate dehydrogenase from Campylobacter jejuni
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative isopropylmalate dehydrogenase
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion 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
3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å
AuthorsTkaczuk, K.L. / Chruszcz, M. / Grimshaw, S. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of putative 3-isopropylmalate dehydrogenase from Campylobacter jejuni
Authors: Tkaczuk, K.L. / Chruszcz, M. / Grimshaw, S. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _struct_ref_seq_dif.details
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: 3-isopropylmalate dehydrogenase
D: 3-isopropylmalate dehydrogenase
E: 3-isopropylmalate dehydrogenase
F: 3-isopropylmalate dehydrogenase
G: 3-isopropylmalate dehydrogenase
H: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,60315
Polymers317,1968
Non-polymers4087
Water32,7151816
1
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4234
Polymers79,2992
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-29 kcal/mol
Surface area28410 Å2
MethodPISA
2
C: 3-isopropylmalate dehydrogenase
D: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3964
Polymers79,2992
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-35 kcal/mol
Surface area28110 Å2
MethodPISA
3
E: 3-isopropylmalate dehydrogenase
hetero molecules

G: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4234
Polymers79,2992
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4480 Å2
ΔGint-25 kcal/mol
Surface area28480 Å2
MethodPISA
4
F: 3-isopropylmalate dehydrogenase
hetero molecules

H: 3-isopropylmalate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,3613
Polymers79,2992
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4240 Å2
ΔGint-27 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.717, 83.170, 111.204
Angle α, β, γ (deg.)94.19, 90.07, 89.64
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39649.438 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: leuB, Cj1718c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9PLW0, 3-isopropylmalate dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1816 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25%PEG3350, 0.2M Na Chloride, 0.1MHEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 213853 / Num. obs: 213853 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 18.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2 / Num. unique all: 10781 / Rsym value: 0.554 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
DMmodel building
MLPHAREphasing
RESOLVEmodel building
CCP4model building
ARP/wARPmodel building
REFMAC5.6.0117refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1CM7

1cm7


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23639 10935 5.1 %RANDOM
Rwork0.19749 ---
all0.19951 205131 --
obs0.19951 205131 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.991 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20.18 Å20.25 Å2
2---2.97 Å2-0.13 Å2
3---3.57 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21851 0 25 1816 23692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01922222
X-RAY DIFFRACTIONr_bond_other_d00.0214952
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.98230004
X-RAY DIFFRACTIONr_angle_other_deg4.332336850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00452831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25225.781948
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.133154048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.411576
X-RAY DIFFRACTIONr_chiral_restr0.1120.23445
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0224632
X-RAY DIFFRACTIONr_gen_planes_other0.0140.024104
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 824 -
Rwork0.286 15194 -
obs--94.92 %

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