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- PDB-6hxp: Structure of citryl-CoA lyase from Hydrogenobacter thermophilus -

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Basic information

Entry
Database: PDB / ID: 6hxp
TitleStructure of citryl-CoA lyase from Hydrogenobacter thermophilus
ComponentsCitryl-CoA lyase
KeywordsLYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


citrate synthase activity / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle / lyase activity
Similarity search - Function
Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COENZYME A / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsVerstraete, K. / Verschueren, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders1524918N Belgium
CitationJournal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: 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: Citryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8724
Polymers29,9121
Non-polymers9603
Water3,801211
1
A: Citryl-CoA lyase
hetero molecules

A: Citryl-CoA lyase
hetero molecules

A: Citryl-CoA lyase
hetero molecules

A: Citryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,48716
Polymers119,6494
Non-polymers3,83912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area31440 Å2
ΔGint-310 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.596, 130.596, 83.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

21A-530-

HOH

31A-595-

HOH

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Components

#1: Protein Citryl-CoA lyase


Mass: 29912.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Gene: ccl / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q75VX1
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 45% MPD 0.1 M HEPES pH 7.5 200 mM NH4 acetate Protein sample buffer 20 mM HEPES, 150 mM NaCl, pH 7.4 supplemented with 10 mM CoASH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.45→48 Å / Num. all: 122838 / Num. obs: 63972 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.77 Å2 / CC1/2: 1 / Rrim(I) all: 0.059 / Net I/σ(I): 16.29
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 19899 / CC1/2: 0.47 / Rrim(I) all: 2.02 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACL holoenzyme structure from C. limicola

Resolution: 1.45→47.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.965 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.046 / SU Rfree Blow DPI: 0.047 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3140 4.91 %RANDOM
Rwork0.145 ---
obs0.146 63952 99.9 %-
Displacement parametersBiso mean: 36.91 Å2
Baniso -1Baniso -2Baniso -3
1-3.9871 Å20 Å20 Å2
2--3.9871 Å20 Å2
3----7.9743 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: 1 / Resolution: 1.45→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 58 211 2275
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014287HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037836HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1011SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes649HARMONIC5
X-RAY DIFFRACTIONt_it4287HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion13.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4937SEMIHARMONIC4
LS refinement shellResolution: 1.45→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 248 5.4 %
Rwork0.229 4341 -
all0.23 4589 -
obs--98.62 %
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)
11.6240.1235-0.36282.1017-0.48160.9347-0.00840.07830.09840.08370.05940.3214-0.1528-0.0501-0.0509-0.02230.00560.0219-0.0858-0.01810.01944.855825.4554-39.7952
21.6286-1.2349-0.88582.23380.53151.230.0116-0.10470.04450.2935-0.0649-0.1269-0.07950.09060.05330.0145-0.0184-0.01070.0097-0.02710.003520.746218.2502-33.4161
31.16620.5431-0.02591.15520.06290.87860.02810.0122-0.14640.05470.018-0.16530.02880.0659-0.0462-0.04150.0052-0.0054-0.0254-0.01340.017210.4102-1.4155-42.569
42.5041-0.54860.32971.2661-0.62373.0676-0.0245-0.5436-0.00140.53960.00950.30830.0733-0.05280.0150.1557-0.04250.02950.0143-0.0033-0.201514.33048.4388-12.6948
54.98540.5583-1.4962.4684-0.49243.6253-0.166-0.3949-0.40440.3091-0.011-0.31080.40060.31680.177-0.0360.0214-0.0547-0.07010.0352-0.121625.04757.6107-23.1565
61.7224-1.16391.33090.1917-2.58362.39620.0531-0.4980.09190.2801-0.0804-0.07230.07750.19150.02720.1362-0.0066-0.09380.05830.0165-0.170123.5827.9537-12.508
70.78890.23040.22091.310.31140.6402-0.0074-0.0392-0.08720.2312-0.0264-0.03480.060.06810.0338-0.0226-0.00270.0047-0.051-0.0099-0.01915.34347.2531-32.5389
80.7427-0.8470.82980.0791-0.46221.2145-0.02910.1245-0.4832-0.24480.1114-0.19020.00760.2333-0.0823-0.08930.02890.0374-0.0483-0.10560.198211.9667-16.9633-49.6563
90.14541.6491-0.22343.74810.28090.3622-0.0291-0.03060.03020.1710.077-0.54340.18240.095-0.04790.01010.0166-0.0393-0.11890.01970.0453-5.9613-32.9625-39.016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|3 - A|47 }
2X-RAY DIFFRACTION2{ A|48 - A|61 }
3X-RAY DIFFRACTION3{ A|62 - A|100 }
4X-RAY DIFFRACTION4{ A|101 - A|129 }
5X-RAY DIFFRACTION5{ A|130 - A|163 }
6X-RAY DIFFRACTION6{ A|164 - A|180 }
7X-RAY DIFFRACTION7{ A|181 - A|228 }
8X-RAY DIFFRACTION8{ A|229 - A|241 }
9X-RAY DIFFRACTION9{ A|242 - A|259 }

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