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- PDB-4adm: Crystal structure of Rv1098c in complex with meso-tartrate -

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Basic information

Entry
Database: PDB / ID: 4adm
TitleCrystal structure of Rv1098c in complex with meso-tartrate
ComponentsFUMARATE HYDRATASE CLASS II
KeywordsLYASE / TRICARBOXYLIC ACID CYCLE / FUMARASE
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) / 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
S,R MESO-TARTARIC ACID / Fumarate hydratase class II / Fumarate hydratase class II
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMechaly, A.E. / Haouz, A. / Miras, I. / Weber, P. / Shepard, W. / Cole, S. / Alzari, P.M. / Bellinzoni, M.
CitationJournal: FEBS Lett. / Year: 2012
Title: Conformational Changes Upon Ligand Binding in the Essential Class II Fumarase Rv1098C from Mycobacterium Tuberculosis.
Authors: Mechaly, A.E. / Haouz, A. / Miras, I. / Barilone, N. / Weber, P. / Shepard, W. / Alzari, P.M. / Bellinzoni, M.
History
DepositionDec 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: FUMARATE HYDRATASE CLASS II
C: FUMARATE HYDRATASE CLASS II
D: FUMARATE HYDRATASE CLASS II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,3638
Polymers210,8784
Non-polymers4844
Water30,4271689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29830 Å2
ΔGint-153.1 kcal/mol
Surface area53650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.940, 96.490, 139.650
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FUMARATE HYDRATASE CLASS II / FUMARASE C


Mass: 52719.566 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O53446, UniProt: P9WN93*PLUS, fumarate hydratase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1689 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.05 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→39.64 Å / Num. obs: 277914 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 23.04 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NO9

3no9


Resolution: 1.65→24.16 Å / Cor.coef. Fo:Fc: 0.9568 / Cor.coef. Fo:Fc free: 0.9463 / SU R Cruickshank DPI: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.071
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 13967 5.05 %RANDOM
Rwork0.1627 ---
obs0.1639 276381 99.51 %-
Displacement parametersBiso mean: 28.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.9896 Å20 Å2-0.5485 Å2
2---0.7254 Å20 Å2
3----0.2642 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 1.65→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13321 0 32 1689 15042
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113553HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9718438HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6337SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes345HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2022HARMONIC5
X-RAY DIFFRACTIONt_it13553HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion2.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1895SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact18514SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2259 1008 4.92 %
Rwork0.2081 19491 -
all0.2089 20499 -
obs--99.51 %
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)
11.2359-0.21970.1880.68170.45721.7499-0.0014-0.10070.1987-0.01220.0307-0.184-0.20710.2628-0.0293-0.0672-0.0526-0.03260.0206-0.025-0.000481.52711.423942.0977
20.9776-0.21260.07580.26910.02250.3643-0.0361-0.15010.13150.05270.0417-0.013-0.08520.0164-0.0056-0.03470.0183-0.0373-0.0089-0.019-0.073555.664111.475948.4834
31.055-0.656-0.57420.91171.30881.2153-0.0034-0.0859-0.10740.02750.0538-0.04890.08230.1656-0.0504-0.0260.037-0.04650.07940.0117-0.067772.21570.934957.4679
40.9489-0.20080.13410.2407-0.01720.4672-0.0084-0.05070.080.00810.00740.0025-0.06480.01090.001-0.01850.0152-0.0335-0.016-0.004-0.047649.819411.49841.0434
51.6661.02830.1091.94750.03791.23-0.0823-0.21530.0638-0.07320.02140.2021-0.0948-0.24060.0609-0.10060.1208-0.01040.10260.00180.027712.55115.777744.1731
62.9529-1.14930.40991.86970.33723.0011-0.0567-0.2296-0.06740.04070.01060.2628-0.1281-0.33240.0461-0.09660.10350.02020.11290.01770.00925.346815.881746.9824
72.1417-1.2715-1.03811.9267-0.45431.20320.00760.1522-0.205-0.09910.0910.56840.2306-0.3914-0.0987-0.11-0.0626-0.06650.02360.00710.102513.2997-9.826232.0103
81.0427-0.11640.16050.6234-0.37691.3659-0.0479-0.2228-0.29540.10390.04390.21730.1446-0.2590.0039-0.0734-0.02290.02110.06220.07610.06317.7114-9.688147.4486
91.1568-0.25650.00570.3506-0.02710.3954-0.0519-0.2703-0.17260.08060.07490.06470.0538-0.0391-0.023-0.04710.0302-0.02140.01190.054-0.061147.3184-10.261652.6119
100.8676-0.24580.0040.41070.01210.4235-0.012-0.0801-0.14470.02660.03050.06330.076-0.0336-0.0185-0.00590.011-0.0311-0.00150.0215-0.009148.2235-11.671940.8389
111.95220.53640.40921.34290.1270.8629-0.0703-0.1463-0.1233-0.06640.063-0.13650.06330.18150.0073-0.07910.1017-0.03640.08290.0046-0.035285.4686-15.800443.9675
123.0207-1.0843-0.49721.8366-0.45922.3276-0.029-0.2189-0.10550.02260.0297-0.23490.22150.299-0.0007-0.0890.0992-0.07650.108-0.0214-0.0193.2209-15.845246.335
130.4248-0.2471-0.55591.90060.70780.20170.0015-0.06470.06520.0819-0.0120.1277-0.1009-0.09760.01050.3334-0.1932-0.1407-0.0917-0.08010.038156.405343.228734.6769
141.2750.5876-1.06252.5572-2.94797.20620.1166-0.05390.13660.2915-0.1678-0.0087-0.70570.50050.0512-0.0202-0.0329-0.06-0.0942-0.0181-0.082157.790330.347931.6615
150.52440.04170.03431.0739-0.32083.1465-0.04660.03710.1461-0.08770.0483-0.0878-0.43520.1858-0.00170.0653-0.0441-0.0337-0.08720.0224-0.010755.947532.884417.289
160.4369-0.21420.03930.7154-0.08470.22070.01910.12820.0062-0.1296-0.0056-0.06780.01460.0608-0.01350.01130.0167-0.0218-0.0083-0.0031-0.057260.8613-1.075915.0239
171.2704-0.3743-0.90531.7747-0.2380.4079-0.09620.07210.2258-0.10620.0763-0.00750.0216-0.06340.01990.07390.0144-0.062-0.0240.0458-0.051848.428423.54666.2155
180.6507-0.16660.05320.4287-0.01850.4155-0.00210.02080.0023-0.04880.0219-0.0523-0.01310.0729-0.0198-0.04710.01-0.0275-0.0438-0.0046-0.07962.8810.57425.3487
191.4207-0.20470.07456.6738-2.72897.89350.0585-0.1608-0.2092-0.38710.1396-0.49811.0507-0.0403-0.19810.11550.0283-0.0577-0.1308-0.05010.057674.0335-40.331519.1834
202.1191-0.15980.16362.31491.50374.9579-0.0032-0.1161-0.28870.23140.03550.20090.8822-0.4543-0.03220.0922-0.0814-0.0417-0.0740.05840.027239.2592-32.926832.245
210.53730.09360.10021.14920.13633.6268-0.02330.0624-0.1716-0.16030.05660.20380.5307-0.1909-0.03330.0637-0.0498-0.0813-0.1243-0.01730.033742.06-32.528117.0001
220.5418-0.37340.03621.07090.2120.27070.01810.0913-0.0671-0.1087-0.00330.16250.0128-0.0433-0.01480.00120.0109-0.0559-0.01960.0024-0.049337.13291.39115.0514
232.4244-1.4721.28572.0907-0.36891.70350.02340.1724-0.145-0.0884-0.0793-0.0560.03950.07490.05590.0620.013-0.044-0.0383-0.0522-0.046649.5536-23.14055.9515
240.6887-0.21220.03680.50830.03010.4491-0.0024-0.0023-0.0357-0.03070.01670.09880.009-0.0781-0.0143-0.04520.0089-0.0443-0.0390.0007-0.04935.1302-0.36425.3594
250.9204-0.6914-0.05087.57022.36936.40080.0415-0.07670.2337-0.35310.0910.4951-0.8743-0.0082-0.13240.10.0393-0.065-0.12110.04520.100223.863440.855619.8015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 9:99
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 100:221
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 222:259
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 260:393
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 394:423
6X-RAY DIFFRACTION6CHAIN A AND RESSEQ 424:467
7X-RAY DIFFRACTION7CHAIN B AND RESSEQ 9:44
8X-RAY DIFFRACTION8CHAIN B AND RESSEQ 45:144
9X-RAY DIFFRACTION9CHAIN B AND RESSEQ 145:259
10X-RAY DIFFRACTION10CHAIN B AND RESSEQ 260:393
11X-RAY DIFFRACTION11CHAIN B AND RESSEQ 394:423
12X-RAY DIFFRACTION12CHAIN B AND RESSEQ 424:466
13X-RAY DIFFRACTION13CHAIN C AND RESSEQ 10:23
14X-RAY DIFFRACTION14CHAIN C AND RESSEQ 24:48
15X-RAY DIFFRACTION15CHAIN C AND RESSEQ 49:137
16X-RAY DIFFRACTION16CHAIN C AND RESSEQ 138:232
17X-RAY DIFFRACTION17CHAIN C AND RESSEQ 233:260
18X-RAY DIFFRACTION18CHAIN C AND RESSEQ 261:399
19X-RAY DIFFRACTION19CHAIN C AND RESSEQ 400:465
20X-RAY DIFFRACTION20CHAIN D AND RESSEQ 10:48
21X-RAY DIFFRACTION21CHAIN D AND RESSEQ 49:137
22X-RAY DIFFRACTION22CHAIN D AND RESSEQ 138:232
23X-RAY DIFFRACTION23CHAIN D AND RESSEQ 233:260
24X-RAY DIFFRACTION24CHAIN D AND RESSEQ 261:399
25X-RAY DIFFRACTION25CHAIN D AND RESSEQ 400:465

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