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- PDB-4e3e: CRYSTAL STRUCTURE OF putative MaoC domain protein dehydratase fro... -

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Basic information

Entry
Database: PDB / ID: 4e3e
TitleCRYSTAL STRUCTURE OF putative MaoC domain protein dehydratase from Chloroflexus aurantiacus J-10-fl
ComponentsMaoC domain protein dehydratase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / protein dehydratase / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


2-methylfumaryl-CoA hydratase / carbon fixation by 3-hydroxypropionate cycle / oxo-acid-lyase activity / glyoxylate catabolic process
Similarity search - Function
: / Mesaconyl-CoA hydratase / Thiol ester hydratase, Rv0216, predicted / : / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Beta-methylmalyl-CoA dehydratase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative MaoC domain protein dehydratase from Chloroflexus aurantiacus J-10-fl
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MaoC domain protein dehydratase
B: MaoC domain protein dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1564
Polymers77,9642
Non-polymers1922
Water8,647480
1
A: MaoC domain protein dehydratase
hetero molecules

A: MaoC domain protein dehydratase
hetero molecules

A: MaoC domain protein dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2346
Polymers116,9463
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9930 Å2
ΔGint-72 kcal/mol
Surface area35960 Å2
MethodPISA
2
B: MaoC domain protein dehydratase
hetero molecules

B: MaoC domain protein dehydratase
hetero molecules

B: MaoC domain protein dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2346
Polymers116,9463
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9900 Å2
ΔGint-73 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.438, 133.438, 170.798
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

21A-714-

HOH

31B-692-

HOH

Detailstrimer

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Components

#1: Protein MaoC domain protein dehydratase


Mass: 38982.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: Caur_0173 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A9WC34
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M sodium citrate:citric acid, pH 5.5, 40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 27.61 / Number: 742528 / Rmerge(I) obs: 0.069 / Χ2: 1.53 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 178479 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165098.810.0312.0464.3
4.095.1698.610.0382.4794.1
3.584.0999.810.0522.8694.2
3.253.5899.910.062.7154.2
3.023.2510010.072.1594.3
2.843.0210010.0771.6824.3
2.72.8410010.0921.5194.3
2.582.710010.1081.4174.3
2.482.5810010.1351.3324.3
2.392.4810010.1621.2664.3
2.322.3910010.2011.2254.2
2.252.3210010.2311.2414.2
2.192.2510010.2611.1874.2
2.142.1910010.31.1784.2
2.092.1410010.3641.1234.1
2.052.0910010.4521.0484.1
2.012.0510010.5351.0124.1
1.972.0110010.6470.9514
1.931.9799.910.7130.9323.8
1.91.9398.210.8110.9223.5
ReflectionResolution: 1.9→50 Å / Num. obs: 178479 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Χ2: 1.53 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.933.50.81188700.922198.2
1.93-1.973.80.71388500.932199.9
1.97-2.0140.64789040.9511100
2.01-2.054.10.53589961.0121100
2.05-2.094.10.45289561.0481100
2.09-2.144.10.36489621.1231100
2.14-2.194.20.388451.1781100
2.19-2.254.20.26190441.1871100
2.25-2.324.20.23189021.2411100
2.32-2.394.20.20189261.2251100
2.39-2.484.30.16289651.2661100
2.48-2.584.30.13589351.3321100
2.58-2.74.30.10889141.4171100
2.7-2.844.30.09289761.5191100
2.84-3.024.30.07789711.6821100
3.02-3.254.30.0789092.1591100
3.25-3.584.20.0689472.715199.9
3.58-4.094.20.05289282.869199.8
4.09-5.164.10.03888412.479198.6
5.16-504.30.03188382.046198.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.41 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.1387 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8358 / SU B: 6.284 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1194 / SU Rfree: 0.0967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 4475 5 %RANDOM
Rwork0.1406 ---
obs0.143 89193 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 36.3421 Å2 / Biso min: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 10 480 5944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025629
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.957685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34222.7263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74215829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2331551
X-RAY DIFFRACTIONr_chiral_restr0.0820.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214375
X-RAY DIFFRACTIONr_rigid_bond_restr3.88635629
X-RAY DIFFRACTIONr_sphericity_free35.1835197
X-RAY DIFFRACTIONr_sphericity_bonded19.35355776
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 332 -
Rwork0.287 6179 -
all-6511 -
obs--99.5 %
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)
10.4946-0.2096-0.06260.52740.0460.12590.00180.02280.0263-0.0453-0.00730.13730.0153-0.00580.00550.10110.0002-0.01520.11020.00290.0522-19.82776.4176147.3522
20.7309-0.08-0.09810.427-0.04470.13310.0045-0.0428-0.10940.0217-0.0182-0.07910.00310.00070.01370.1010.0003-0.00910.09990.0120.039115.4633-13.9669100.8929
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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