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- PDB-3cux: Atomic Resolution Structures of Escherichia coli and Bacillis ant... -

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Basic information

Entry
Database: PDB / ID: 3cux
TitleAtomic Resolution Structures of Escherichia coli and Bacillis anthracis Malate Synthase A: Comparison with Isoform G and Implications for Structure Based Drug Design
ComponentsMalate synthase
KeywordsTRANSFERASE / malate synthase / TIM barrel / Glyoxylate bypass / Tricarboxylic acid cycle
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Malate synthase A / Malate synthase, conserved site / Malate synthase signature. / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel ...Malate synthase A / Malate synthase, conserved site / Malate synthase signature. / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / 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
Malate synthase / Malate synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLohman, J.R. / Remington, S.J.
CitationJournal: Protein Sci. / Year: 2008
Title: Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery
Authors: Lohman, J.R. / Olson, A.C. / Remington, S.J.
History
DepositionApr 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 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)60,5693
Polymers60,5201
Non-polymers492
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.865, 52.036, 89.107
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

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Components

#1: Protein Malate synthase /


Mass: 60520.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TEV cleavable / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: aceB / Plasmid: pBAD / Production host: Escherichia coli (E. coli)
References: UniProt: Q81TX1, UniProt: A0A6L8PPD0*PLUS, malate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.85 Å3/Da / Density % sol: 33.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M sodium citrate, 0.1M Tris pH8.0, 30% PEG 1550, 30mM nickel chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2007
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 43852 / Num. obs: 43852 / % possible obs: 89.9 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 62.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Escherichia coli malate synthase isoform A

Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.174 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23536 2200 5 %RANDOM
Rwork0.20072 ---
obs0.20246 41639 89.7 %-
all-41639 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å22.63 Å2
2---1.31 Å20 Å2
3---2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 2 168 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9515521
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9815507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13223.97199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50915710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0891530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22049
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22807
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0251.52570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50324006
X-RAY DIFFRACTIONr_scbond_it2.64631720
X-RAY DIFFRACTIONr_scangle_it3.8814.51510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 109 -
Rwork0.252 2052 -
obs-3032 59.89 %

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