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- PDB-5oas: Crystal structure of malate synthase G from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 5oas
TitleCrystal structure of malate synthase G from Pseudomonas aeruginosa in apo form.
ComponentsMalate synthase G
KeywordsTRANSFERASE / GLYOXYLATE SHUNT
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate catabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / cytosol
Similarity search - Function
Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel ...Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMcVey, A.C. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Commission624620 United Kingdom
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Functional Characterization of Malate Synthase G from Opportunistic Pathogen Pseudomonas aeruginosa.
Authors: McVey, A.C. / Medarametla, P. / Chee, X. / Bartlett, S. / Poso, A. / Spring, D.R. / Rahman, T. / Welch, M.
History
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 19, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 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: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,47622
Polymers79,1281
Non-polymers1,34821
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint17 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.171, 81.197, 137.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Malate synthase G


Mass: 79128.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: glcB, PA0482
Variant: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I636, malate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.51 Å3/Da / Density % sol: 51.03 % / Description: Orthorhombic
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: PEG 4000 ammonium sulfate glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.62→69.962 Å / Num. obs: 95973 / % possible obs: 94.19 % / Observed criterion σ(F): 1.35 / Redundancy: 5.8 % / Biso Wilson estimate: 19.6 Å2 / Net I/σ(I): 11.75

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 1.62→69.926 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.1934 4713 4.91 %
Rwork0.167 --
obs0.1683 95973 94.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→69.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5555 0 86 691 6332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085724
X-RAY DIFFRACTIONf_angle_d0.8977719
X-RAY DIFFRACTIONf_dihedral_angle_d15.493429
X-RAY DIFFRACTIONf_chiral_restr0.055860
X-RAY DIFFRACTIONf_plane_restr0.0061017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6198-1.63820.3488880.3431954X-RAY DIFFRACTION61
1.6382-1.65750.3186960.33262104X-RAY DIFFRACTION65
1.6575-1.67770.30411110.32522267X-RAY DIFFRACTION72
1.6777-1.69890.33391360.31622459X-RAY DIFFRACTION77
1.6989-1.72130.32391420.30842585X-RAY DIFFRACTION81
1.7213-1.74490.28091330.29562768X-RAY DIFFRACTION87
1.7449-1.76980.30891360.27522925X-RAY DIFFRACTION91
1.7698-1.79620.32881650.25793030X-RAY DIFFRACTION95
1.7962-1.82430.30881550.23993180X-RAY DIFFRACTION98
1.8243-1.85420.26441470.2173169X-RAY DIFFRACTION100
1.8542-1.88620.22551470.21263227X-RAY DIFFRACTION100
1.8862-1.92050.24841920.18983170X-RAY DIFFRACTION100
1.9205-1.95740.21451510.18813186X-RAY DIFFRACTION100
1.9574-1.99740.21662070.17923174X-RAY DIFFRACTION100
1.9974-2.04080.22111690.17293223X-RAY DIFFRACTION100
2.0408-2.08830.20111790.16823156X-RAY DIFFRACTION100
2.0883-2.14050.19491660.15793214X-RAY DIFFRACTION100
2.1405-2.19840.18561910.15753189X-RAY DIFFRACTION100
2.1984-2.26310.17951700.15343207X-RAY DIFFRACTION100
2.2631-2.33610.21141580.15973231X-RAY DIFFRACTION100
2.3361-2.41960.20511540.15393228X-RAY DIFFRACTION100
2.4196-2.51650.18481800.1553226X-RAY DIFFRACTION100
2.5165-2.63110.18451650.15253250X-RAY DIFFRACTION100
2.6311-2.76980.18211730.1443233X-RAY DIFFRACTION100
2.7698-2.94330.16731600.14293238X-RAY DIFFRACTION100
2.9433-3.17060.181770.13973275X-RAY DIFFRACTION100
3.1706-3.48960.14881520.14433284X-RAY DIFFRACTION100
3.4896-3.99460.15641770.13623300X-RAY DIFFRACTION100
3.9946-5.03250.14981570.1353329X-RAY DIFFRACTION100
5.0325-69.99160.18491790.18053479X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.9589 Å / Origin y: 74.9668 Å / Origin z: 49.8051 Å
111213212223313233
T0.1468 Å2-0.0524 Å2-0.0219 Å2-0.1325 Å20.0064 Å2--0.1098 Å2
L0.5803 °2-0.0723 °20.0124 °2-0.6762 °20.0359 °2--0.5211 °2
S-0.024 Å °0.0639 Å °-0.0056 Å °-0.0911 Å °0.0228 Å °-0.0441 Å °-0.1369 Å °0.0917 Å °-0.0035 Å °
Refinement TLS groupSelection details: all

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