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- PDB-3no9: Crystal Structure of apo fumarate hydratase from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 3no9
TitleCrystal Structure of apo fumarate hydratase from Mycobacterium tuberculosis
ComponentsFumarate hydratase class II
KeywordsLYASE / apo / Structural Genomics / TB Structural Genomics Consortium / fumarate hydratase / tricarboxylic acid cycle / lyase class I / TBSGC
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / 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 / Fumarate lyase, conserved site ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / 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 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fumarate hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLi, H. / Swanson, S. / Yu, M. / Hung, L.-W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of apo fumarate hydratase from Mycobacterium tuberculosis
Authors: Li, H. / Swanson, S. / Yu, M. / Hung, L.-H. / Sacchettini, J.S.
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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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


Theoretical massNumber of molelcules
Total (without water)201,1164
Polymers201,1164
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25090 Å2
ΔGint-137 kcal/mol
Surface area57520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)271.224, 96.555, 89.889
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...
211CHAIN B AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...
311CHAIN C AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...
411CHAIN D AND (RESSEQ 21:232 OR RESSEQ 241: 313 OR...

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Components

#1: Protein
Fumarate hydratase class II / Fumarase C


Mass: 50278.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fum, fumC, MT1130, MTV017.51c, Rv1098c / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 18% PEG 400, 0.1M sodium acetate pH 4.5, 0.2M calcium chloride, drop ratio 1:1, protein concentration 8mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2007
Details: VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR
RadiationMonochromator: LIQUID NITROGEN COOLED DUAL CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→48.523 Å / Num. obs: 70730 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 40.99 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 8.6
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.39 / Rsym value: 0.414 / % possible all: 71.9

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YFE

1yfe


Resolution: 2.48→48.52 Å / SU ML: 0.25 / σ(F): 1.91 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 3533 5 %
Rwork0.206 --
obs0.208 70709 88.4 %
all-70773 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.56 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4885 Å2-0 Å2-2.1327 Å2
2---5.8135 Å20 Å2
3---6.302 Å2
Refinement stepCycle: LAST / Resolution: 2.48→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13421 0 0 178 13599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813630
X-RAY DIFFRACTIONf_angle_d1.05818528
X-RAY DIFFRACTIONf_dihedral_angle_d14.3644958
X-RAY DIFFRACTIONf_chiral_restr0.0722214
X-RAY DIFFRACTIONf_plane_restr0.0042451
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2787X-RAY DIFFRACTIONPOSITIONAL
12B2787X-RAY DIFFRACTIONPOSITIONAL0.052
13C2787X-RAY DIFFRACTIONPOSITIONAL0.052
14D2787X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4826-2.51660.3138570.24981066X-RAY DIFFRACTION36
2.5166-2.55250.30731150.23872163X-RAY DIFFRACTION71
2.5525-2.59060.31531320.24972228X-RAY DIFFRACTION74
2.5906-2.63110.31221420.24042227X-RAY DIFFRACTION74
2.6311-2.67430.27611160.22992284X-RAY DIFFRACTION76
2.6743-2.72040.24681140.21852387X-RAY DIFFRACTION78
2.7204-2.76980.2761530.222428X-RAY DIFFRACTION81
2.7698-2.82310.24641140.22672460X-RAY DIFFRACTION81
2.8231-2.88070.29661100.21692583X-RAY DIFFRACTION84
2.8807-2.94330.24361360.222605X-RAY DIFFRACTION86
2.9433-3.01180.27471190.21072701X-RAY DIFFRACTION88
3.0118-3.08710.22871390.21382766X-RAY DIFFRACTION92
3.0871-3.17060.2641660.21922841X-RAY DIFFRACTION95
3.1706-3.26380.25041420.22192968X-RAY DIFFRACTION97
3.2638-3.36920.25261600.22563007X-RAY DIFFRACTION99
3.3692-3.48960.25961430.20443021X-RAY DIFFRACTION99
3.4896-3.62920.2411690.193014X-RAY DIFFRACTION99
3.6292-3.79430.21221530.1943047X-RAY DIFFRACTION100
3.7943-3.99430.20321610.17863035X-RAY DIFFRACTION100
3.9943-4.24440.2281620.17643044X-RAY DIFFRACTION100
4.2444-4.57190.20311900.16382983X-RAY DIFFRACTION100
4.5719-5.03160.20391730.1693048X-RAY DIFFRACTION99
5.0316-5.75860.21771550.19063058X-RAY DIFFRACTION100
5.7586-7.25140.23421350.21093096X-RAY DIFFRACTION100
7.2514-48.53260.26111770.23373116X-RAY DIFFRACTION99

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