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- PDB-3q94: The crystal structure of fructose 1,6-bisphosphate aldolase from ... -

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Basic information

Entry
Database: PDB / ID: 3q94
TitleThe crystal structure of fructose 1,6-bisphosphate aldolase from Bacillus anthracis str. 'Ames Ancestor'
ComponentsFructose-bisphosphate aldolase, class II
KeywordsLYASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha-Beta Barrel / cytoplasmic
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-1,6-bisphosphate aldolase, class 2 / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / ACETATE ION / Fructose-bisphosphate aldolase / Fructose-bisphosphate aldolase, class II
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.301 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of fructose 1,6-bisphosphate aldolase from Bacillus anthracis str. 'Ames Ancestor'.
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.ptnr3_auth_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase, class II
B: Fructose-bisphosphate aldolase, class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,08320
Polymers62,8062
Non-polymers1,27618
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-319 kcal/mol
Surface area21290 Å2
MethodPISA
2
A: Fructose-bisphosphate aldolase, class II
B: Fructose-bisphosphate aldolase, class II
hetero molecules

A: Fructose-bisphosphate aldolase, class II
B: Fructose-bisphosphate aldolase, class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,16640
Polymers125,6134
Non-polymers2,55336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area13360 Å2
ΔGint-664 kcal/mol
Surface area41300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.155, 95.155, 155.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructose-bisphosphate aldolase, class II / / Fructose 1 / 6-bisphosphate aldolase


Mass: 31403.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: fba2, BAS5184, BA_5580, GBAA5580, GBAA_5580 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q81JW4, UniProt: A0A6H3AA11*PLUS, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 383 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M Zn Acetate, 0.1M Na Acetate, 10% PEG 3000, 20mM fructose 1,6-bisphosphate, 20mM D-glyceric acid hemicalcium, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→45.5 Å / Num. all: 36984 / Num. obs: 36984 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.176 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.91 / Num. unique all: 1848 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1RVG

1rvg


Resolution: 2.301→45.507 Å / SU ML: 0.32 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1741 4.98 %Random
Rwork0.1656 ---
all0.1684 34975 --
obs0.1684 34975 94.62 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.477 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.222 Å20 Å20 Å2
2---2.222 Å2-0 Å2
3---4.444 Å2
Refinement stepCycle: LAST / Resolution: 2.301→45.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 48 365 4654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084344
X-RAY DIFFRACTIONf_angle_d1.0355871
X-RAY DIFFRACTIONf_dihedral_angle_d14.1971605
X-RAY DIFFRACTIONf_chiral_restr0.067668
X-RAY DIFFRACTIONf_plane_restr0.005772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3006-2.38280.31291480.22983033X-RAY DIFFRACTION87
2.3828-2.47820.25811610.20273050X-RAY DIFFRACTION89
2.4782-2.5910.26611500.18363177X-RAY DIFFRACTION91
2.591-2.72760.2791570.1833224X-RAY DIFFRACTION93
2.7276-2.89850.27151680.17523318X-RAY DIFFRACTION95
2.8985-3.12220.22481980.17633322X-RAY DIFFRACTION96
3.1222-3.43630.2691660.17163456X-RAY DIFFRACTION98
3.4363-3.93330.20541890.15513465X-RAY DIFFRACTION99
3.9333-4.95460.16782050.12353513X-RAY DIFFRACTION99
4.9546-45.51610.18021990.16083676X-RAY DIFFRACTION99
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)
10.22190.2664-0.2480.3731-0.11650.3599-0.00080.01320.0588-0.010.01470.0618-0.04350.024900.0660.01190.0020.07230.01940.0843-20.881163.127738.9844
20.3691-0.0093-0.05560.3517-0.0920.24670.0478-0.0704-0.0564-0.0518-0.0010.00790.0126-0.04670.07910.051-0.004-0.01270.08160.02660.0587-33.777533.917160.0166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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