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- PDB-3kx6: Crystal structure of fructose-1,6-bisphosphate aldolase from Babe... -

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Basic information

Entry
Database: PDB / ID: 3kx6
TitleCrystal structure of fructose-1,6-bisphosphate aldolase from Babesia bovis at 2.1A resolution
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald Biostructures / Babesia bovis / fructose-1 / 6-bisphosphate aldolase / Glycolysis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesBabesia bovis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of fructose-1,6-bisphosphate aldolase from Babesia bovis at 2.1A resolution
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Edwards, T.E. / Staker, B.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,52515
Polymers165,1434
Non-polymers1,38111
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint3 kcal/mol
Surface area46530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.880, 114.160, 174.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 341
2115B1 - 341
3115C1 - 341
4115D1 - 341

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Components

#1: Protein
Fructose-bisphosphate aldolase


Mass: 41285.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia bovis (eukaryote) / Strain: T2BO / Gene: BBOV_IV000790 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7AV51, fructose-bisphosphate aldolase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: EBS CRYO SCREEN H12: 50% PEG 200, 100MM PHOSPHATE/CITRATE PH 4.2, 200MM NACL; BABOA.00974.A AT 30MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.975484 / Wavelength: 0.975484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975484 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 100767 / Num. obs: 99984 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 33.47 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 5.1 / Num. unique all: 7365 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PC4 modified with CCP4 program CHAINSAW

2pc4


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.386 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, tls / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4992 5 %RANDOM
Rwork0.16 ---
all0.162 100767 --
obs0.162 99909 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-0 Å2
2--1.74 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10279 0 92 805 11176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210629
X-RAY DIFFRACTIONr_bond_other_d0.0010.027042
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.97514433
X-RAY DIFFRACTIONr_angle_other_deg0.949317298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69651397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23224.955444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.399151760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.121560
X-RAY DIFFRACTIONr_chiral_restr0.0850.21676
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021993
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_it0.6961.56865
X-RAY DIFFRACTIONr_mcbond_other0.2241.52801
X-RAY DIFFRACTIONr_mcangle_it1.293210979
X-RAY DIFFRACTIONr_scbond_it2.28833764
X-RAY DIFFRACTIONr_scangle_it3.7814.53438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1978medium positional0.150.5
B1978medium positional0.250.5
C1978medium positional0.130.5
D1978medium positional0.320.5
A2156loose positional0.355
B2156loose positional0.45
C2156loose positional0.345
D2156loose positional0.475
A1978medium thermal0.562
B1978medium thermal0.852
C1978medium thermal0.742
D1978medium thermal0.62
A2156loose thermal0.7410
B2156loose thermal0.8910
C2156loose thermal0.7510
D2156loose thermal0.7310
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 359 -
Rwork0.169 6918 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4586-0.20050.3180.5654-0.09961.09530.0578-0.0274-0.0524-0.07220.02920.07180.1345-0.2091-0.0870.0547-0.0514-0.0240.06690.0310.040261.027101.19629.869
20.3866-0.00380.05620.35210.20981.1179-0.003-0.0341-0.01450.04290.02310.0382-0.0229-0.1708-0.02010.07110.02810.03940.04130.01950.023169.079114.3866.855
30.9377-0.04690.41550.60150.14911.1110.01790.0813-0.04880.0880.0323-0.07260.16620.2485-0.05020.08120.0535-0.02780.0746-0.03410.0426106.37498.26756.911
40.4023-0.1208-0.20220.4275-0.28511.19560.06350.08590.0801-0.0115-0.0695-0.0925-0.05340.24260.0060.0587-0.03410.0360.14690.01010.052998.902117.97422.424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 358
2X-RAY DIFFRACTION1A400 - 401
3X-RAY DIFFRACTION1A359 - 907
4X-RAY DIFFRACTION2B2 - 358
5X-RAY DIFFRACTION2B400 - 402
6X-RAY DIFFRACTION2B359 - 903
7X-RAY DIFFRACTION3C3 - 358
8X-RAY DIFFRACTION3C400 - 402
9X-RAY DIFFRACTION3C359 - 906
10X-RAY DIFFRACTION4D4 - 358
11X-RAY DIFFRACTION4D400 - 402
12X-RAY DIFFRACTION4D359 - 905

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