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- PDB-6kin: Crystal structure of the tri-functional malyl-CoA lyase from Rose... -

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Basic information

Entry
Database: PDB / ID: 6kin
TitleCrystal structure of the tri-functional malyl-CoA lyase from Roseiflexus castenholzii
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Malyl-CoA lyase / CitE-like superfamily / Roseiflexus castenholzii
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesRoseiflexus castenholzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.527 Å
AuthorsTang, W.R. / Zhang, C.Y. / Wang, C. / Xu, X.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31870740 China
National Science Foundation (China)31570738 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The C-terminal domain conformational switch revealed by the crystal structure of malyl-CoA lyase from Roseiflexus castenholzii.
Authors: Tang, W. / Wang, Z. / Zhang, C. / Wang, C. / Min, Z. / Zhang, X. / Liu, D. / Shen, J. / Xu, X.
History
DepositionJul 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
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: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
C: HpcH/HpaI aldolase
D: HpcH/HpaI aldolase
E: HpcH/HpaI aldolase
F: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,1428
Polymers229,8976
Non-polymers2442
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The absorption peak of may-coenzyme A lyase in gel filtration is corresponding to a trimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30570 Å2
ΔGint-168 kcal/mol
Surface area71530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.033, 133.417, 139.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HpcH/HpaI aldolase


Mass: 38316.215 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Strain: DSM 13941 / HLO8 / Gene: Rcas_0912 / Variant: E.coli / Plasmid: pET28a / Production host: Escherichia coli 042 (bacteria) / References: UniProt: A7NHT0
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The protein sample was mixed with an equal volume of the reservoir solution (16 % (v/v) PEG3350 and 0.2 M sodium chloride), and the mixture was equilibrated against the reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97893 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 73219 / % possible obs: 96.6 % / Redundancy: 4.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.387 / Num. unique obs: 3642 / CC1/2: 0.905 / Rpim(I) all: 0.186 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L7Z

4l7z


Resolution: 2.527→48.225 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.15
RfactorNum. reflection% reflection
Rfree0.2337 3613 4.94 %
Rwork0.1756 --
obs0.1784 73110 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.01 Å2 / Biso mean: 50.0814 Å2 / Biso min: 28.14 Å2
Refinement stepCycle: final / Resolution: 2.527→48.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16016 0 16 293 16325
Biso mean--39.54 48.95 -
Num. residues----2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816525
X-RAY DIFFRACTIONf_angle_d0.92622456
X-RAY DIFFRACTIONf_chiral_restr0.0522448
X-RAY DIFFRACTIONf_plane_restr0.0072948
X-RAY DIFFRACTIONf_dihedral_angle_d5.0249934
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5272-2.56050.3283900.2324167760
2.5605-2.59550.30981210.2241272897
2.5955-2.63260.29961240.2285270898
2.6326-2.67190.28361520.2226269198
2.6719-2.71370.28691320.2184274998
2.7137-2.75810.29191550.2171272599
2.7581-2.80570.29761540.2201268597
2.8057-2.85670.28961320.2134272997
2.8567-2.91160.27341590.2254269597
2.9116-2.97110.3171400.2194272098
2.9711-3.03570.29931600.2153269898
3.0357-3.10630.26881480.2081271797
3.1063-3.18390.26061530.207269897
3.1839-3.270.26761650.1984268197
3.27-3.36620.26841370.1977272797
3.3662-3.47480.28481320.202272897
3.4748-3.5990.22441400.1802270297
3.599-3.7430.23881410.164273197
3.743-3.91330.25621390.1675271996
3.9133-4.11950.22341470.1595269496
4.1195-4.37750.1741150.1406274696
4.3775-4.71520.16951200.1407271696
4.7152-5.18920.16191330.142271795
5.1892-5.93890.22191360.1601267994
5.9389-7.47790.20271460.1694271093
7.4779-48.2250.19711420.1491272790

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