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- PDB-3q3w: Isopropylmalate isomerase small subunit from Campylobacter jejuni. -

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Basic information

Entry
Database: PDB / ID: 3q3w
TitleIsopropylmalate isomerase small subunit from Campylobacter jejuni.
Components3-isopropylmalate dehydratase small subunit
KeywordsTRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / isopropylmalate / isomerase
Function / homologyAconitase; domain 4 / Aconitase, domain 4 / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsOsipiuk, J. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Isopropylmalate isomerase small subunit from Campylobacter jejuni.
Authors: Osipiuk, J. / Gu, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-isopropylmalate dehydratase small subunit
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)46,5932
Polymers46,5932
Non-polymers00
Water3,837213
1
A: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)23,2961
Polymers23,2961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-isopropylmalate dehydratase small subunit


Theoretical massNumber of molelcules
Total (without water)23,2961
Polymers23,2961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.496, 151.937, 32.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 3-isopropylmalate dehydratase small subunit / Alpha-IPM isomerase / Isopropylmalate isomerase


Mass: 23296.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: subsp. jejuni IA3902 / Gene: CJSA_1625, leuD / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3FPI3, 3-isopropylmalate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M trisodium citrate dihydrate, 20% PEG-3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→41.9 Å / Num. all: 29037 / Num. obs: 29037 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.095 / Χ2: 1.187 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.89-1.926.40.8272.2913771.01989.7
1.92-1.966.70.73513951.09494
1.96-270.60913631.10591.5
2-2.047.10.49614091.18290.1
2.04-2.087.20.44813921.15493.6
2.08-2.137.40.40113571.24290
2.13-2.187.40.33913851.25389.6
2.18-2.247.30.30813901.31893
2.24-2.317.30.26513901.25290.7
2.31-2.387.30.23114071.22693.4
2.38-2.477.20.19914281.2292.9
2.47-2.577.20.16614501.23594.5
2.57-2.687.20.1414471.21294.2
2.68-2.827.10.12714741.18996.7
2.82-36.90.10915091.1796
3-3.2370.0914921.18596.7
3.23-3.566.90.07615201.15497
3.56-4.076.70.06715411.17897.5
4.07-5.136.60.05615901.1599.7
5.13-506.50.05317211.1799.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2HCU

2hcu


Resolution: 1.89→41.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.28 / SU B: 8.85 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1464 5.1 %RANDOM
Rwork0.1869 ---
obs0.1892 28862 92.93 %-
all-28862 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.93 Å2 / Biso mean: 31.707 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--2.33 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.89→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 0 213 3111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223114
X-RAY DIFFRACTIONr_bond_other_d0.0010.022146
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9624231
X-RAY DIFFRACTIONr_angle_other_deg0.91935294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65125.528161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94215596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9061511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_mcbond_it0.9831.51858
X-RAY DIFFRACTIONr_mcbond_other0.2751.5751
X-RAY DIFFRACTIONr_mcangle_it1.70723020
X-RAY DIFFRACTIONr_scbond_it2.65931256
X-RAY DIFFRACTIONr_scangle_it4.0964.51186
LS refinement shellResolution: 1.89→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 96 -
Rwork0.303 1753 -
all-1849 -
obs-1849 81.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1424-0.06860.97381.9560.03220.9849-0.1201-0.5297-0.23310.01420.04610.1542-0.0544-0.31870.0740.04680.04280.01920.21510.0630.089532.238721.563132.6295
20.9256-0.2143-0.02721.6728-0.3821.73660.0134-0.01540.12250.04380.0545-0.1016-0.0994-0.0202-0.06780.0655-0.02040.00160.03850.03210.06727.023460.420914.8743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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