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- PDB-2g4o: anomalous substructure of 3-ISOPROPYLMALATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 2g4o
Titleanomalous substructure of 3-ISOPROPYLMALATE DEHYDROGENASE
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / anomalous substructure of 3-ISOPROPYLMALATE DEHYDROGENASE
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
3-isopropylmalate dehydrogenase, actinobacteria / : / 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 / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: 3-isopropylmalate dehydrogenase
D: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,14512
Polymers141,7404
Non-polymers4058
Water9,602533
1
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1087
Polymers70,8702
Non-polymers2385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-80 kcal/mol
Surface area25200 Å2
MethodPISA
2
C: 3-isopropylmalate dehydrogenase
D: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0375
Polymers70,8702
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-58 kcal/mol
Surface area25360 Å2
MethodPISA
3
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules

C: 3-isopropylmalate dehydrogenase
D: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,14512
Polymers141,7404
Non-polymers4058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area12340 Å2
ΔGint-152 kcal/mol
Surface area47700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.570, 98.580, 184.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35435.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: leuB / Production host: Escherichia coli (E. coli)
References: UniProt: P95313, UniProt: P9WKK9*PLUS, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.51 Å3/Da / Density % sol: 51.05 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 97028 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.298 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26011 2045 2.1 %RANDOM
Rwork0.20941 ---
obs0.21043 94983 99.86 %-
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 mean: 43.784 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2--1.19 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9972 0 16 533 10521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02110224
X-RAY DIFFRACTIONr_bond_other_d0.0010.029696
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.96413934
X-RAY DIFFRACTIONr_angle_other_deg0.939322290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87451349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84822.598435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.929151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.13115107
X-RAY DIFFRACTIONr_chiral_restr0.1070.21645
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022084
X-RAY DIFFRACTIONr_nbd_refined0.230.22379
X-RAY DIFFRACTIONr_nbd_other0.1920.210127
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24994
X-RAY DIFFRACTIONr_nbtor_other0.0870.26430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2910.2546
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.231
X-RAY DIFFRACTIONr_mcbond_it1.4811.58475
X-RAY DIFFRACTIONr_mcbond_other0.2661.52781
X-RAY DIFFRACTIONr_mcangle_it1.9732.510731
X-RAY DIFFRACTIONr_scbond_it4.43353840
X-RAY DIFFRACTIONr_scangle_it6.239103202
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 154 -
Rwork0.279 6894 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.1374 Å / Origin y: 53.602 Å / Origin z: 5.1051 Å
111213212223313233
T-0.183 Å20.0339 Å2-0.0007 Å2--0.1612 Å20.0182 Å2---0.0743 Å2
L1.0234 °20.1964 °2-1.0968 °2-0.4986 °2-0.3957 °2--3.7968 °2
S0.0786 Å °-0.1414 Å °-0.0217 Å °0.0539 Å °0.0166 Å °0.1521 Å °-0.0432 Å °-0.289 Å °-0.0952 Å °

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