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- PDB-3rrp: Crystal structure of fumarate hydratase Fum from Mycobacterium ab... -

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Basic information

Entry
Database: PDB / ID: 3rrp
TitleCrystal structure of fumarate hydratase Fum from Mycobacterium abscessus with malate bound
ComponentsProbable fumarate hydratase Fum
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / tuberculosis / fumerate / malic acid
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
(2S)-2-hydroxybutanedioic acid / Fumarate hydratase class II
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 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 ...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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Probable fumarate hydratase Fum
B: Probable fumarate hydratase Fum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8217
Polymers99,3672
Non-polymers4545
Water9,692538
1
A: Probable fumarate hydratase Fum
B: Probable fumarate hydratase Fum
hetero molecules

A: Probable fumarate hydratase Fum
B: Probable fumarate hydratase Fum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,64214
Polymers198,7334
Non-polymers90910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area33070 Å2
ΔGint-173 kcal/mol
Surface area51500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.800, 156.920, 57.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 8 - 463 / Label seq-ID: 12 - 467

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable fumarate hydratase Fum


Mass: 49683.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_1250c / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MKP6
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MyabA.01507.a.A1 PW30392 at 29.54 mg/mL against Wizard III/IV screen condition G8, 2.1 M DL Malic acid, pH 7.0 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220029g8, ...Details: MyabA.01507.a.A1 PW30392 at 29.54 mg/mL against Wizard III/IV screen condition G8, 2.1 M DL Malic acid, pH 7.0 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220029g8, 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: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 40352 / Num. obs: 39296 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 24.91 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 11.37
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.3-2.364.80.5273.19129432719271993.1
2.36-2.420.5093.5214458274695.1
2.42-2.490.4334.1914315264095.5
2.49-2.570.3874.7214090264197.1
2.57-2.660.3735.0114082257197.1
2.66-2.750.325.9213558247597
2.75-2.850.2487.2813608240598.5
2.85-2.970.2188.2113442234398.8
2.97-3.10.1859.4413007224898.9
3.1-3.250.15511.2712459217698.7
3.25-3.430.12613.8211701204798.5
3.43-3.640.10915.7910969191696.6
3.64-3.890.08519.619565177695.9
3.89-4.20.07222.19763169697.6
4.2-4.60.06124.29396159799.3
4.6-5.140.06322.668573146599.8
5.14-5.940.07518.8375751304100
5.94-7.270.06420.686340112599.9
7.27-10.290.03731.36505788499.8
10.290.03332.16273752298.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.97 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.41 Å
Translation3 Å47.41 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 3RD8

3rd8


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.1759 / WRfactor Rwork: 0.1381 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8895 / SU B: 11.986 / SU ML: 0.133 / SU R Cruickshank DPI: 0.3667 / SU Rfree: 0.2174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1950 5 %RANDOM
Rwork0.1601 ---
obs0.1624 39144 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.54 Å2 / Biso mean: 17.2985 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---0.94 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 30 538 7329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226892
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9779377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47425.373268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.514151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1831538
X-RAY DIFFRACTIONr_chiral_restr0.090.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215158
X-RAY DIFFRACTIONr_mcbond_it0.4711.54594
X-RAY DIFFRACTIONr_mcangle_it0.83527338
X-RAY DIFFRACTIONr_scbond_it1.70732298
X-RAY DIFFRACTIONr_scangle_it2.7444.52037
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3307 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.150.5
MEDIUM THERMAL0.592
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 129 -
Rwork0.186 2577 -
all-2706 -
obs--92.8 %
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)
10.4182-0.0762-0.13840.74850.05190.7609-0.00680.02240.078-0.00830.00330.0431-0.083-0.16140.00350.02610.03210.00730.04540.00790.0679-14.171331.627-20.2422
20.3187-0.0977-0.03930.78190.08180.48750.0073-0.02710.05250.02470.01770.0481-0.0349-0.0706-0.02510.03870.02640.00710.0425-0.00360.0312-12.222528.9393-6.004
30.00630.0342-0.01030.2141-0.02730.09930.0022-0.01740.00230.0169-0.01610.01930.0049-0.01590.01390.04220.00160.00540.04760.00120.0486-11.0224-0.476-9.4018
40.8804-0.7733-0.0362.07150.09050.376-0.0277-0.0824-0.17360.0650.04030.11660.0954-0.0438-0.01260.0601-0.0360.00590.0430.01440.0353-14.2933-36.642-8.889
53.7703-1.2749-2.94958.7989-2.14163.35870.1534-0.04160.23950.1438-0.0186-0.2943-0.1792-0.0456-0.13480.0203-0.0195-0.02430.1532-0.01730.1196-43.06270.0032-21.7184
60.59320.07020.16620.3179-0.0030.7559-0.0430.00890.0372-0.00870.00290.0354-0.0572-0.07130.04010.01170.0051-0.00510.03580.00940.0614-32.79043.6362-34.4327
70.08440.06610.03020.10680.01250.0724-0.01620.01310.0149-0.00040.00450.021-0.0243-0.01540.01170.045-0.00090.00210.03540.00350.0431.261512.6263-35.0704
85.19930.4995-0.7871.059-0.03372.4081-0.04220.32420.0412-0.0355-0.0418-0.0862-0.14980.06750.0840.0282-0.01120.01880.02390.0080.071539.991724.6849-36.8983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 51
2X-RAY DIFFRACTION2A52 - 158
3X-RAY DIFFRACTION3A159 - 379
4X-RAY DIFFRACTION4A380 - 467
5X-RAY DIFFRACTION5B6 - 18
6X-RAY DIFFRACTION6B19 - 142
7X-RAY DIFFRACTION7B143 - 426
8X-RAY DIFFRACTION8B427 - 465

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