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- PDB-4l80: Crystal Structure of Chloroflexus aurantiacus malyl-CoA lyase in ... -

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Basic information

Entry
Database: PDB / ID: 4l80
TitleCrystal Structure of Chloroflexus aurantiacus malyl-CoA lyase in complex with magnesium, oxalate, and propionyl-CoA
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


malyl-CoA lyase / carbon fixation by 3-hydroxypropionate cycle / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / oxaloacetate metabolic process / magnesium ion binding / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / 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
propionyl Coenzyme A / OXALATE ION / Malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase / Malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.008 Å
AuthorsZarzycki, J. / Kerfeld, C.A.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.
Authors: Zarzycki, J. / Kerfeld, C.A.
History
DepositionJun 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 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)236,35226
Polymers230,4926
Non-polymers5,86020
Water30,4271689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37360 Å2
ΔGint-223 kcal/mol
Surface area66020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.151, 102.151, 204.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 38415.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: OK-70-fl / Gene: Caur_0174, mcl / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A9WC35, UniProt: S5N020*PLUS, malyl-CoA lyase

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Non-polymers , 5 types, 1709 molecules

#2: Chemical
ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40N7O17P3S
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M sodium cacodylate, pH 5.5, 20% w/v PEG4000) + 1 part ...Details: 1 part protein solution (7.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 2 parts buffer (0.1 M sodium cacodylate, pH 5.5, 20% w/v PEG4000) + 1 part substrate solution (20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride, 20 mM propionyl-CoA, 25 mM sodium oxalate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2012
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.008→37.93 Å / Num. all: 138647 / Num. obs: 138647 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rsym value: 0.106 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.008-2.125.10.6371.2101851201270.63799.2
2.12-2.245.10.4381.797257190430.43899.8
2.24-2.45.10.3022.591858179810.30299.9
2.4-2.595.10.2153.585847167820.21599.9
2.59-2.845.10.151579165154500.151100
2.84-3.175.10.1017.571386139540.101100
3.17-3.675.10.0612.662620123430.06100
3.67-4.4950.0372051806104300.037100
4.49-6.3550.0323.54015480940.03100
6.35-37.935.10.02231.32250344430.02299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8.2_1303refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L7Z

4l7z


Resolution: 2.008→37.93 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.2 / σ(F): 1.18 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1983 1.45 %
Rwork0.1725 --
obs0.1729 138596 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.91 Å2 / Biso mean: 28.2585 Å2 / Biso min: 8.57 Å2
Refinement stepCycle: LAST / Resolution: 2.008→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16114 0 370 1689 18173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616910
X-RAY DIFFRACTIONf_angle_d0.90723016
X-RAY DIFFRACTIONf_chiral_restr0.0592500
X-RAY DIFFRACTIONf_plane_restr0.0032994
X-RAY DIFFRACTIONf_dihedral_angle_d15.7316314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.008-2.0320.27191300.26229267939796
2.032-2.05780.25971460.26039610975699
2.0578-2.08480.33791410.24449622976399
2.0848-2.11340.28581420.24679449959199
2.1134-2.14360.26041380.24019565970399
2.1436-2.17560.28431460.23279681982799
2.1756-2.20960.26721420.22239539968199
2.2096-2.24580.24111350.20939596973199
2.2458-2.28450.23391390.21049626976599
2.2845-2.3260.23751420.19399635977799
2.326-2.37080.24631360.19489563969999
2.3708-2.41920.23671450.19459554969999
2.4192-2.47180.25841440.19179640978499
2.4718-2.52920.23061460.17939666981299
2.5292-2.59250.22811420.189646978899
2.5925-2.66260.22271480.17729581972999
2.6626-2.74090.19851400.17199697983799
2.7409-2.82930.20591450.16279694983999
2.8293-2.93040.19931370.169496229759100
2.9304-3.04770.19021410.17019654979599
3.0477-3.18630.24671450.167896739818100
3.1863-3.35420.17741370.164296679804100
3.3542-3.56420.1741420.153796559797100
3.5642-3.83920.17821420.139896669808100
3.8392-4.22510.16111410.130297319872100
4.2251-4.83540.12731420.129896239765100
4.8354-6.0880.13061460.149496669812100
6.088-37.9370.15461390.154997229861100

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