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- PDB-4ov9: Structure of isopropylmalate synthase binding with alpha-isopropy... -

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Basic information

Entry
Database: PDB / ID: 4ov9
TitleStructure of isopropylmalate synthase binding with alpha-isopropylmalate
Componentsisopropylmalate synthase
KeywordsTRANSFERASE / alpha/beta Tim barrel
Function / homology
Function and homology information


2-isopropylmalate synthase / 2-isopropylmalate synthase activity / cellular biosynthetic process / : / carboxylic acid metabolic process / metal ion binding
Similarity search - Function
Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid / 2-isopropylmalate synthase
Similarity search - Component
Biological speciesLeptospira biflexa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Z. / Wu, J. / Wang, C. / Zhang, P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Subdomain II of alpha-isopropylmalate synthase is essential for activity: inferring a mechanism of feedback inhibition.
Authors: Zhang, Z. / Wu, J. / Lin, W. / Wang, J. / Yan, H. / Zhao, W. / Ma, J. / Ding, J. / Zhang, P. / Zhao, G.P.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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_seq_id / _struct_conn.ptnr1_label_seq_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_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

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Assembly

Deposited unit
A: isopropylmalate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3933
Polymers46,1511
Non-polymers2422
Water2,666148
1
A: isopropylmalate synthase
hetero molecules

A: isopropylmalate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7866
Polymers92,3032
Non-polymers4834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area5150 Å2
ΔGint-21 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.354, 131.354, 46.719
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein isopropylmalate synthase / Alpha-isopropylmalate synthase Alpha-IPM synthetase


Mass: 46151.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira biflexa (bacteria) / Strain: Patoc 1 / ATCC 23582 / Paris / Gene: IPMS2, LEPBI_I1108, leuA2 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0SN40, 2-isopropylmalate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VPM / (2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.52 Å3/Da / Density % sol: 51.21 % / Mosaicity: 0.337 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 0.8mM sodium formate, 30% PEG 2000 MME, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Dec 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23769 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.122 / Χ2: 0.976 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.285.50.41823600.73799.9
2.28-2.376.10.3623590.67100
2.37-2.486.30.31423580.692100
2.48-2.616.30.2523400.683100
2.61-2.776.30.20423570.733100
2.77-2.996.30.1523540.772100
2.99-3.296.30.12423830.972100
3.29-3.766.30.10123831.412100
3.76-4.746.30.07224071.59100
4.74-506.10.05624681.43299.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.416 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1217 5.1 %RANDOM
Rwork0.1611 ---
obs0.1627 23688 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.98 Å2 / Biso mean: 29.509 Å2 / Biso min: 4.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 13 148 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193019
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9484086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2045378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.11224.632136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8571516
X-RAY DIFFRACTIONr_chiral_restr0.080.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212248
X-RAY DIFFRACTIONr_rigid_bond_restr2.29633018
X-RAY DIFFRACTIONr_sphericity_free17.637544
X-RAY DIFFRACTIONr_sphericity_bonded7.18653072
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 69 -
Rwork0.177 1604 -
all-1673 -
obs--99.52 %

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