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- PDB-6kkh: Crystal structure of the oxalate bound malyl-CoA lyase from Rosei... -

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Basic information

Entry
Database: PDB / ID: 6kkh
TitleCrystal structure of the oxalate bound malyl-CoA lyase from Roseiflexus castenholzii
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / Malyl-CoA lyase / CitE-like superfamily / Roseiflexus castenholzii / Conformational changes
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
OXALATE ION / HpcH/HpaI aldolase
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsTang, W.R. / Wang, Z.G. / Zhang, C.Y. / Wang, C.
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 25, 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 ...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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
G: HpcH/HpaI aldolase
H: HpcH/HpaI aldolase
I: HpcH/HpaI aldolase
J: HpcH/HpaI aldolase
K: HpcH/HpaI aldolase
L: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,68422
Polymers459,79512
Non-polymers88910
Water4,900272
1
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)230,34211
Polymers229,8976
Non-polymers4455
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30380 Å2
ΔGint-183 kcal/mol
Surface area70670 Å2
MethodPISA
2
G: HpcH/HpaI aldolase
H: HpcH/HpaI aldolase
I: HpcH/HpaI aldolase
J: HpcH/HpaI aldolase
K: HpcH/HpaI aldolase
L: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,34211
Polymers229,8976
Non-polymers4455
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30400 Å2
ΔGint-177 kcal/mol
Surface area70440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.899, 156.652, 155.090
Angle α, β, γ (deg.)90.000, 98.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HpcH/HpaI aldolase / malyl-CoA lyase


Mass: 38316.215 Da / Num. of mol.: 12
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7NHT0
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: The RfxMCL was incubated with Maganesium ion, oxalate and propionyl-CoA at a 1:1.5:1.5 molar ratio before crystallization to obtain the crystal of RfxMCL-OXL in a reservoir solution ...Details: The RfxMCL was incubated with Maganesium ion, oxalate and propionyl-CoA at a 1:1.5:1.5 molar ratio before crystallization to obtain the crystal of RfxMCL-OXL in a reservoir solution containing 16 % PEG8000, 0.2 M ammonium acetate and 0.1 M Tris pH8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 133993 / % possible obs: 99 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Net I/σ(I): 16.3
Reflection shellResolution: 2.64→2.7 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.21 / Num. unique obs: 6605 / CC1/2: 0.879 / Rsym value: 0.689 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KIN

6kin


Resolution: 2.64→49.48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.101 / SU ML: 0.291 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.35
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 6782 5.1 %RANDOM
Rwork0.1988 ---
obs0.2019 127186 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.17 Å2 / Biso mean: 56.437 Å2 / Biso min: 14.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å2-0.49 Å2
2---1.86 Å20 Å2
3---4.38 Å2
Refinement stepCycle: final / Resolution: 2.64→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31303 0 58 272 31633
Biso mean--53.56 40.52 -
Num. residues----4035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01532154
X-RAY DIFFRACTIONr_bond_other_d0.0010.01729565
X-RAY DIFFRACTIONr_angle_refined_deg0.9111.75443686
X-RAY DIFFRACTIONr_angle_other_deg0.3141.69469080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02354008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35818.7411160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.246154514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.26615211
X-RAY DIFFRACTIONr_chiral_restr0.0380.24143
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02136275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025857
LS refinement shellResolution: 2.64→2.709 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 482 -
Rwork0.283 9000 -
all-9482 -
obs--95.04 %

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