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- PDB-3qbp: Crystal structure of fumarase Fum from Mycobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 3qbp
TitleCrystal structure of fumarase Fum from Mycobacterium marinum
ComponentsFumarase Fum
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / fumarase / Mycobacterium / tuberculosis / non-pathogenic species
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
Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJan 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarase Fum
B: Fumarase Fum
C: Fumarase Fum
D: Fumarase Fum


Theoretical massNumber of molelcules
Total (without water)201,2274
Polymers201,2274
Non-polymers00
Water30,3371684
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25380 Å2
ΔGint-146 kcal/mol
Surface area53220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.880, 114.080, 98.840
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fumarase Fum


Mass: 50306.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: fum, MMAR_4368 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HT54
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1684 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MymaA.01507.a.A1 PS00842 at 51.1 mg/mL against PACT screen condition A7, 0.2 M NaCl, 0.1 M NaOAc pH 5.0, 20% PEG 6000 soaked into PACT A7 with 25% EG as cryo-protectant, crystal tracking ID ...Details: MymaA.01507.a.A1 PS00842 at 51.1 mg/mL against PACT screen condition A7, 0.2 M NaCl, 0.1 M NaOAc pH 5.0, 20% PEG 6000 soaked into PACT A7 with 25% EG as cryo-protectant, crystal tracking ID 218662a7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 176835 / Num. obs: 176663 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.51
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.85-1.94.60.5053.11100
1.9-1.950.4253.71100
1.95-2.010.3374.6199.8
2.01-2.070.275.61100
2.07-2.140.2366.4199.9
2.14-2.210.1848.1199.9
2.21-2.290.169.31100
2.29-2.390.13610.8199.9
2.39-2.490.12211.81100
2.49-2.620.10913.1199.9
2.62-2.760.09115.7199.9
2.76-2.930.07817.9199.9
2.93-3.130.06920.2199.9
3.13-3.380.05424.6199.9
3.38-3.70.04331.1199.9
3.7-4.140.03435.7199.8
4.14-4.780.0339.9199.9
4.78-5.850.03336.2199.9
5.85-8.270.02938.8199.8
8.270.0251.2199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.71 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.71 Å
Translation3 Å48.71 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 3no9, molecule A residues 43 to 393

3no9


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.905 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.188 8834 5 %
Rwork0.155 --
obs0.157 176519 99.9 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 17.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20.79 Å2
2---0.75 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12804 0 0 1684 14488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213296
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.96518180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07951848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66424.934527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.559152159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5331587
X-RAY DIFFRACTIONr_chiral_restr0.0920.22212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110019
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6891.58878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.203214201
X-RAY DIFFRACTIONr_scbond_it234418
X-RAY DIFFRACTIONr_scangle_it3.3574.53933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å
RfactorNum. reflection% reflection
Rfree0.263 672 -
Rwork0.215 12411 -
obs--99.91 %
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)
10.03110.06670.06240.36410.18910.24190.0185-0.0270.00720.0453-0.01510.00430.0334-0.0644-0.00340.0285-0.01180.01090.0415-0.0070.0078-36.7949-18.5342-11.5332
20.31480.06560.03930.12840.03550.03970.00240.03530.0089-0.0234-0.0056-0.01050.01950.00520.00330.02820.00370.01030.03180.00180.0108-21.3901-18.9778-42.456
30.33160.37430.15410.65080.29950.20860.0277-0.0316-0.07110.0348-0.0164-0.11760.03090.0087-0.01120.02750.0068-0.00650.00860.00940.0505-11.4131-21.957-13.7955
40.4170.07070.08280.1162-0.01240.0802-0.00520.00710.09260.0029-0.00490.028-0.0128-0.00770.01010.0090.01010.00270.01310.00430.0422-27.8143.1923-30.7345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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