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- PDB-3oyx: Haloferax volcanii Malate Synthase Magnesium/Glyoxylate Complex -

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Basic information

Entry
Database: PDB / ID: 3oyx
TitleHaloferax volcanii Malate Synthase Magnesium/Glyoxylate Complex
ComponentsMalate synthase
KeywordsTRANSFERASE / TIM barrel / glyoxylate complex
Function / homology
Function and homology information


malate synthase / malate synthase activity / oxaloacetate metabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / metal ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1560 / : / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1560 / : / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / : / Malate synthase
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsHoward, B.R. / Bracken, C. / Neighbor, A. / Thomas, G. / Lamlenn, K.K. / Schubert, H.L. / Whitby, F.G.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G.
Authors: Bracken, C.D. / Neighbor, A.M. / Lamlenn, K.K. / Thomas, G.C. / Schubert, H.L. / Whitby, F.G. / Howard, B.R.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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

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Assembly

Deposited unit
A: Malate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,53412
Polymers48,0671
Non-polymers46711
Water2,414134
1
A: Malate synthase
hetero molecules

A: Malate synthase
hetero molecules

A: Malate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,60136
Polymers144,2013
Non-polymers1,40133
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16760 Å2
ΔGint-179 kcal/mol
Surface area41590 Å2
MethodPISA
2
A: Malate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)291,20372
Polymers288,4016
Non-polymers2,80266
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area43070 Å2
ΔGint-396 kcal/mol
Surface area73630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.023, 155.023, 141.787
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-703-

CL

21A-434-

HOH

31A-524-

HOH

41A-541-

HOH

51A-554-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Malate synthase


Mass: 48066.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloferax volcanii (archaea) / Strain: ATCC 29605, DS2 / References: UniProt: D4GTL2, malate synthase

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Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: PEG 4500, glycerol, 2M KCl,MgCl2, pH 4.4, supplemented with 0.1M glyoxylate, 0.1M MgCl2, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 21, 2010 / Details: R-axis IV, confocal optics
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 22203 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.096 / Χ2: 1.024 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.593.20.45320201.039190
2.59-2.693.40.3922281.0451100
2.69-2.813.40.29622441.0371100
2.81-2.963.40.21522481.0371100
2.96-3.153.40.16422401.018199.9
3.15-3.393.40.12922481.032199.7
3.39-3.733.40.09722570.979199.5
3.73-4.263.40.08222411.051199.3
4.26-5.353.40.06822591.042198.3
5.35-203.50.04922180.964194.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.67 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.65 Å29.1 Å
Translation2.65 Å29.1 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2683 / WRfactor Rwork: 0.2134 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8279 / SU B: 7.332 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2727 / SU Rfree: 0.2355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1109 5 %RANDOM
Rwork0.1921 ---
obs0.1948 22200 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 119.47 Å2 / Biso mean: 58.333 Å2 / Biso min: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 19 134 2882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212825
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9563836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.925353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92224.702151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8615460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2311522
X-RAY DIFFRACTIONr_chiral_restr0.1210.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212241
X-RAY DIFFRACTIONr_mcbond_it1.081.51740
X-RAY DIFFRACTIONr_mcangle_it2.00922802
X-RAY DIFFRACTIONr_scbond_it3.07631085
X-RAY DIFFRACTIONr_scangle_it4.9314.51030
LS refinement shellResolution: 2.51→2.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 73 -
Rwork0.243 1476 -
all-1549 -
obs--96.09 %

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