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- PDB-3tv2: Structure of a class II fumarate hydratase from Burkholderia pseu... -

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Basic information

Entry
Database: PDB / ID: 3tv2
TitleStructure of a class II fumarate hydratase from Burkholderia pseudomallei
ComponentsFumarate hydratase, class IIFumarase
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / fumarase
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Fumarate hydratase class II
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of a class II fumarate hydratase from Burkholderia pseudomallei
Authors: Clifton, M.C. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Sankaran, B.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_atom_id / _struct_conn.ptnr1_label_seq_id / _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: Fumarate hydratase, class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7903
Polymers48,7671
Non-polymers232
Water8,305461
1
A: Fumarate hydratase, class II
hetero molecules

A: Fumarate hydratase, class II
hetero molecules

A: Fumarate hydratase, class II
hetero molecules

A: Fumarate hydratase, class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,16112
Polymers195,0694
Non-polymers928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area28710 Å2
ΔGint-220 kcal/mol
Surface area53180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.180, 147.180, 208.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-31-

HOH

21A-41-

HOH

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Components

#1: Protein Fumarate hydratase, class II / Fumarase


Mass: 48767.305 Da / Num. of mol.: 1 / Fragment: UNP residues 145-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: fumC, BURPS1710b_2940 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JQ34, fumarate hydratase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 6.68 Å3/Da / Density % sol: 81.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium citrate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350, protein 18.9 mg/mL, 25% ethylene glycol cryoprotectant, TargetDB ID: BupsA.00047.a.D13 PD00173, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→99.99 Å / Num. obs: 76331 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.66
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.5093.72199.2
2.15-2.210.4124.57199.1
2.21-2.280.3415.8198.6
2.28-2.350.2756.93199.2
2.35-2.420.2367.97199.4
2.42-2.510.1899.76199.4
2.51-2.60.16511.4199.2
2.6-2.710.12914.67198.9
2.71-2.830.10817.12199
2.83-2.970.08621198.8
2.97-3.130.07324.82198.4
3.13-3.320.0630.05198.1
3.32-3.550.04837.51197.4
3.55-3.830.0445.14196.5
3.83-4.20.03254.16196.1
4.2-4.70.02959.73195.1
4.7-5.420.02858.42193.6
5.42-6.640.02955.2193
6.64-9.390.0273.21191.2
9.390.01776.54186.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.85 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.8 Å
Translation3 Å19.8 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YFE

1yfe


Resolution: 2.1→48.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.675 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0903 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17592 3841 5.1 %RANDOM
Rwork0.15566 ---
obs0.15666 76047 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 2 461 3847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193497
X-RAY DIFFRACTIONr_bond_other_d0.0010.022288
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9464766
X-RAY DIFFRACTIONr_angle_other_deg0.98235594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85424.156154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9691525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214023
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02698
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 274 -
Rwork0.235 4937 -
obs--98.82 %
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)
14.3916-3.88622.34695.43150.26344.088-0.5047-0.26750.37410.16870.3106-0.2191-0.4202-0.05490.19410.254-0.0211-0.19350.15140.05390.164819.122673.8551.8186
21.02340.63120.42690.46440.2720.8338-0.03820.12640.0082-0.10840.06870.0144-0.0687-0.0374-0.03050.12940.0521-0.04580.1418-0.00820.061616.916859.52515.1065
31.0251-0.25260.41010.1931-0.12880.35060.02010.0382-0.0324-0.0829-0.02780.00090.08810.00930.00780.08660.0398-0.01120.0807-0.00490.096934.338546.744125.697
40.5453-0.24510.09720.4636-0.08190.0771-0.0676-0.035-0.04880.06020.0203-0.06050.03040.00030.04730.11210.08010.01590.09340.00820.111653.205343.36836.0635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 173
2X-RAY DIFFRACTION2A174 - 275
3X-RAY DIFFRACTION3A276 - 465
4X-RAY DIFFRACTION4A466 - 601

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