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- PDB-3oyz: Haloferax volcanii Malate Synthase Pyruvate/Acetyl-CoA Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 3oyz
TitleHaloferax volcanii Malate Synthase Pyruvate/Acetyl-CoA Ternary Complex
ComponentsMalate Synthase
KeywordsTRANSFERASE / TIM Barrel
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
ACETYL COENZYME *A / : / PHOSPHATE ION / PYRUVIC ACID / Malate synthase
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)49,34312
Polymers48,0671
Non-polymers1,27611
Water3,171176
1
A: Malate Synthase
hetero molecules

A: Malate Synthase
hetero molecules

A: Malate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,02936
Polymers144,2013
Non-polymers3,82833
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 area19950 Å2
ΔGint-205 kcal/mol
Surface area42310 Å2
MethodPISA
2
A: Malate Synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)296,05772
Polymers288,4016
Non-polymers7,65666
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 area49650 Å2
ΔGint-455 kcal/mol
Surface area74850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.788, 154.788, 142.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-800-

PO4

21A-800-

PO4

31A-511-

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 , 7 types, 187 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: PEG 4500, glycerol, 2M KCl,MgCl2 , pH 4.4, supplemented with 0.07M pyruvate, 0.15M acetyl-coa, 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 RAXIS IV / Detector: IMAGE PLATE / Date: Dec 30, 2009 / Details: confocal
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 47508 / Num. obs: 47508 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.25
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.35 / Num. unique all: 47508 / Rsym value: 0.806 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model built into a lower resolution dataset from a crystal soaked under different conditions, phased with a lead derivative using the SIRAS method and SOLVE.

Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.205 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 2404 5.1 %RANDOM
Rwork0.20294 ---
obs0.2047 45068 99.91 %-
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 mean: 47.651 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 70 176 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4671.9794175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78524.522157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12315505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6611525
X-RAY DIFFRACTIONr_chiral_restr0.1770.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6591.51875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.66223009
X-RAY DIFFRACTIONr_scbond_it4.14631201
X-RAY DIFFRACTIONr_scangle_it6.1524.51164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 178 -
Rwork0.303 3246 -
obs--99.51 %

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