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- PDB-7miw: Crystal Structure of Fumarate hydratase class II from Elizabethki... -

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Basic information

Entry
Database: PDB / ID: 7miw
TitleCrystal Structure of Fumarate hydratase class II from Elizabethkingia anophelis NUHP1
ComponentsFumarate hydratase class II
KeywordsLYASE / SSGCID / Elizabethkingia anophelis / NUPH1 / Fumarate hydratase class II / fumC / Aerobic fumarase / tricarboxylic acid cycle / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
Fumarate hydratase class II
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Fumarate hydratase class II from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarate hydratase class II
B: Fumarate hydratase class II
C: Fumarate hydratase class II
D: Fumarate hydratase class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,9226
Polymers206,7984
Non-polymers1242
Water45,5602529
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30260 Å2
ΔGint-185 kcal/mol
Surface area55190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.760, 92.650, 98.430
Angle α, β, γ (deg.)116.151, 107.668, 90.032
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase


Mass: 51699.590 Da / Num. of mol.: 4 / Fragment: ElanA.00047.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: fumC, BD94_3912 / Plasmid: ElanA.00047.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077EJP9, fumarate hydratase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2529 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents JCSG TOP96 screen, condition #61/F1: 20% PEG 3350, 200mM Ammonium formate: ElanA.00047.b.B1.PS38159 at 25mg/ml: tray 318833 F1: cryo: 20% EG: puck NDH4-7.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 465944 / % possible obs: 94.2 % / Redundancy: 3.876 % / Biso Wilson estimate: 14.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.044 / Χ2: 0.967 / Net I/σ(I): 20.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.283.330.2664.32331170.9360.31890.6
1.28-1.323.7910.2275.58326360.9590.26491.7
1.32-1.363.9830.1996.61320380.970.2392.3
1.36-1.43.9810.1677.79311490.980.19392.6
1.4-1.443.9810.1448.95303830.9840.16693
1.44-1.493.9770.11311.31295690.990.13193.4
1.49-1.553.9690.09113.86284750.9930.10593.8
1.55-1.613.9660.07816.11276410.9940.0994.2
1.61-1.693.9580.06718.44265670.9960.07894.6
1.69-1.773.9450.05721.4254320.9960.06694.9
1.77-1.863.9360.04824.91244080.9970.05695.3
1.86-1.983.9140.04128.33231180.9980.04895.7
1.98-2.113.8880.03532.83218160.9980.0496.1
2.11-2.283.8640.03136.55204150.9980.03696.5
2.28-2.53.8510.02939.23188600.9990.03396.7
2.5-2.83.8310.02741.13170620.9990.03197.2
2.8-3.233.8270.02443.69151220.9990.02897.5
3.23-3.953.8320.02145.92128740.9990.02597.9
3.95-5.593.8630.0247.4399220.9990.02398
5.59-503.7290.02346.3553400.9980.02796

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_4205refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
ARP/wARPmodel building
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 3tv2 chain A in three domains as per Morda

3tv2


Resolution: 1.25→35.94 Å / SU ML: 0.0891 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 12.5394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1472 10052 2.16 %0
Rwork0.124 455844 --
obs0.1245 465896 94.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.35 Å2
Refinement stepCycle: LAST / Resolution: 1.25→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14084 0 8 2529 16621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006315076
X-RAY DIFFRACTIONf_angle_d0.918320609
X-RAY DIFFRACTIONf_chiral_restr0.08072360
X-RAY DIFFRACTIONf_plane_restr0.00812715
X-RAY DIFFRACTIONf_dihedral_angle_d12.63645763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.17793450.152214452X-RAY DIFFRACTION89.94
1.26-1.280.153430.140614672X-RAY DIFFRACTION91.16
1.28-1.290.15743320.134714730X-RAY DIFFRACTION91.5
1.29-1.310.17163260.134314739X-RAY DIFFRACTION91.99
1.31-1.330.18973930.141414926X-RAY DIFFRACTION92.16
1.33-1.350.16983320.135614759X-RAY DIFFRACTION92.35
1.35-1.370.15913180.130214925X-RAY DIFFRACTION92.67
1.37-1.390.15823580.121414961X-RAY DIFFRACTION92.66
1.39-1.410.16513320.120914852X-RAY DIFFRACTION92.85
1.41-1.430.1473150.122115046X-RAY DIFFRACTION93.16
1.43-1.460.16313190.117515000X-RAY DIFFRACTION93.3
1.46-1.480.13053260.113215012X-RAY DIFFRACTION93.58
1.48-1.510.15193740.112915132X-RAY DIFFRACTION93.73
1.51-1.540.12413420.107515026X-RAY DIFFRACTION93.91
1.54-1.570.1353130.102615327X-RAY DIFFRACTION94.14
1.57-1.610.13543490.104915093X-RAY DIFFRACTION94.45
1.61-1.650.13363640.107915206X-RAY DIFFRACTION94.63
1.65-1.70.13623420.105615270X-RAY DIFFRACTION94.77
1.7-1.750.12653280.110815271X-RAY DIFFRACTION95.01
1.75-1.80.1383360.115215428X-RAY DIFFRACTION95.33
1.8-1.870.15323250.120615379X-RAY DIFFRACTION95.57
1.87-1.940.14163230.123115435X-RAY DIFFRACTION95.74
1.94-2.030.1653210.128515431X-RAY DIFFRACTION96.13
2.03-2.140.13353110.123915544X-RAY DIFFRACTION96.32
2.14-2.270.13462900.124415590X-RAY DIFFRACTION96.73
2.27-2.450.15093470.123815657X-RAY DIFFRACTION96.94
2.45-2.690.14163270.127715680X-RAY DIFFRACTION97.3
2.69-3.080.13613310.132415744X-RAY DIFFRACTION97.71
3.08-3.880.15213610.124615808X-RAY DIFFRACTION98.17
3.88-35.940.1583290.134615749X-RAY DIFFRACTION97.84

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