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- PDB-5tao: Haloferax volcanii Malate Synthase Lead(II) complex -

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Basic information

Entry
Database: PDB / ID: 5tao
TitleHaloferax volcanii Malate Synthase Lead(II) complex
ComponentsMalate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1560 / HpcH/HpaI aldolase/citrate lyase family / 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
ACETATE ION / GLYOXYLIC ACID / : / LEAD (II) ION / Malate synthase
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHoward, B.R. / Adams, M.J.
Citation
Journal: The Journal of the Utah Academy / Year: 2016
Title: X-ray analysis of Lead(II) binding to Haloferax volcanii Malate Synthase
Authors: Adams, M.J. / Howard, B.R.
#1: Journal: 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 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Structure summary
Revision 1.2Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,45917
Polymers48,0671
Non-polymers1,39216
Water4,576254
1
A: Malate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)296,753102
Polymers288,4016
Non-polymers8,35296
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 area49070 Å2
ΔGint-318 kcal/mol
Surface area78770 Å2
MethodPISA
2
A: Malate synthase
hetero molecules

A: Malate synthase
hetero molecules

A: Malate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,37751
Polymers144,2013
Non-polymers4,17648
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 area19350 Å2
ΔGint-135 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.353, 155.353, 139.412
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-513-

CL

21A-702-

HOH

31A-834-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Malate synthase / / MSH


Mass: 48066.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (archaea)
Strain: ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2
Gene: aceB, aceB1, HVO_1983, C498_05196 / Production host: Haloferax volcanii (archaea) / References: UniProt: D4GTL2, malate synthase

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Non-polymers , 7 types, 270 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE / Glyoxylic acid


Mass: 74.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H2O3
#4: Chemical
ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#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 / Chloride


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: magnesium chloride, glyoxylate, Tris, KCl, ammonium acetate, PEG 4500, glycerol, sodium acetate trihydrate
PH range: 4.4-5.0

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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: Mar 15, 2009 / Details: Rigaku Varimax-HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→96.81 Å / Num. obs: 35791 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.103 / Net I/av σ(I): 11.453 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.183.60.3741100
2.18-2.263.60.315199.9
2.26-2.373.60.2431100
2.37-2.493.70.2041100
2.49-2.653.70.1661100
2.65-2.853.70.1341100
2.85-3.143.70.105199.9
3.14-3.593.80.08199.6
3.59-4.523.80.078199.2
4.52-303.90.099196.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.86 Å29.8 Å
Translation6.86 Å29.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PUG

3pug


Resolution: 2.1→96.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.507 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21668 1880 5 %RANDOM
Rwork0.18308 ---
obs0.18477 35791 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.764 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→96.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 31 254 3080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192927
X-RAY DIFFRACTIONr_bond_other_d0.0010.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.963975
X-RAY DIFFRACTIONr_angle_other_deg0.94436124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43424.744156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21415483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8261523
X-RAY DIFFRACTIONr_chiral_restr0.1140.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
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_it4.3044.5931443
X-RAY DIFFRACTIONr_mcbond_other4.3024.5891441
X-RAY DIFFRACTIONr_mcangle_it5.386.8631802
X-RAY DIFFRACTIONr_mcangle_other5.3796.8651803
X-RAY DIFFRACTIONr_scbond_it5.2935.0661484
X-RAY DIFFRACTIONr_scbond_other5.2825.0651484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3327.4192168
X-RAY DIFFRACTIONr_long_range_B_refined9.25638.0813666
X-RAY DIFFRACTIONr_long_range_B_other9.22937.7083570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.096→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 118 -
Rwork0.23 2649 -
obs--98.72 %

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