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- PDB-5dni: Crystal structure of Methanocaldococcus jannaschii Fumarate hydra... -

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Basic information

Entry
Database: PDB / ID: 5dni
TitleCrystal structure of Methanocaldococcus jannaschii Fumarate hydratase beta subunit
ComponentsPutative L(+)-tartrate dehydratase subunit beta
KeywordsLYASE / alpha beta barrel
Function / homology
Function and homology information


L(+)-tartrate dehydratase / L(+)-tartrate dehydratase activity
Similarity search - Function
fumarase / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain / Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily / Fumarase C-terminus / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative L(+)-tartrate dehydratase subunit beta
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJayaraman, V. / Kunala, J. / Balaram, H.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Biochemistry / Year: 2023
Title: Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin.
Authors: Bellur, A. / Das, S. / Jayaraman, V. / Behera, S. / Suryavanshi, A. / Balasubramanian, S. / Balaram, P. / Jindal, G. / Balaram, H.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Putative L(+)-tartrate dehydratase subunit beta
B: Putative L(+)-tartrate dehydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,73811
Polymers40,0422
Non-polymers6969
Water2,576143
1
A: Putative L(+)-tartrate dehydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4396
Polymers20,0211
Non-polymers4185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint1 kcal/mol
Surface area7900 Å2
MethodPISA
2
B: Putative L(+)-tartrate dehydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2995
Polymers20,0211
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-3 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.610, 85.610, 121.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative L(+)-tartrate dehydratase subunit beta / Putative fumarate hydratase subunit beta / L-TTD beta


Mass: 20021.168 Da / Num. of mol.: 2 / Fragment: UNP residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MjFHbeta, MJ0617 / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q58034, L(+)-tartrate dehydratase

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Non-polymers , 5 types, 152 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.5 / Details: 0.1MBis-Tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 22, 2013
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→60.92 Å / Num. all: 22550 / Num. obs: 22550 / % possible obs: 99.99 % / Redundancy: 4.85 %
Data reduction method: data reduction merge and scaling used SCALA (CCP4)
Rmerge(I) obs: 0.127 / Rrim(I) all: 0.143 / Net I/av σ(I): 4.5853 / Net I/σ(I): 7.0091 / Num. measured all: 109381
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allNum. measured allNum. unique allDiffraction-ID% possible all
2.3-2.424.620.860.891516632821100
2.42-2.574.770.681.12148013104100
2.57-2.754.860.51.55141682916100
2.75-2.974.90.332.32133492727100
2.97-3.254.910.193.89122312490100
3.25-3.644.940.125.81112202271100
3.64-4.24.950.087.8798972000100
4.2-5.144.960.086.9284221699100
5.14-7.274.970.087.3965471317100
7.27-60.924.810.0412.77358074499.73

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata collection
SCALACCP4_3.3.22data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
SCALAdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ISB

2isb


Resolution: 2.3→28.022 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1101 4.9 %
Rwork0.1807 --
obs0.183 22451 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→28.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 44 143 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082827
X-RAY DIFFRACTIONf_angle_d1.1763816
X-RAY DIFFRACTIONf_dihedral_angle_d12.6031020
X-RAY DIFFRACTIONf_chiral_restr0.046437
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40470.35741350.28442675X-RAY DIFFRACTION100
2.4047-2.53140.32211340.26762660X-RAY DIFFRACTION100
2.5314-2.68990.29191150.25012670X-RAY DIFFRACTION100
2.6899-2.89740.32151450.23072646X-RAY DIFFRACTION100
2.8974-3.18860.27721630.21112665X-RAY DIFFRACTION100
3.1886-3.64920.22021340.18112653X-RAY DIFFRACTION100
3.6492-4.59430.19641360.13922676X-RAY DIFFRACTION100
4.5943-28.02450.16821390.14292705X-RAY DIFFRACTION100

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