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- PDB-5u7s: Crystal structure of a fructose-bisphosphate aldolase, class II, ... -

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Basic information

Entry
Database: PDB / ID: 5u7s
TitleCrystal structure of a fructose-bisphosphate aldolase, class II, Calvin cycle subtype from Acinetobacter baumannii
ComponentsFructose-1,6-bisphosphate aldolase
KeywordsLYASE / structural genomics / aldolase / National Institute of Allergy and Infectious Diseases / NIAID / ESKAPE pathogen / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-bisphosphate aldolase, class II, Calvin cycle subtype / 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
CITRIC ACID / FORMIC ACID / Fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a fructose-bisphosphate aldolase, class II, Calvin cycle subtype from Acinetobacter baumannii
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1185
Polymers76,8572
Non-polymers2613
Water1,31573
1
A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
hetero molecules

A: Fructose-1,6-bisphosphate aldolase
B: Fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,23710
Polymers153,7144
Non-polymers5226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12240 Å2
ΔGint-84 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.110, 83.120, 99.390
Angle α, β, γ (deg.)90.000, 131.980, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -2 through 0 or (resid 1...
21(chain B and ((resid -2 through -1 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and (resid -2 through 0 or (resid 1...AA-2 - 06 - 8
12METMETALAALA(chain A and (resid -2 through 0 or (resid 1...AA1 - 29 - 10
13HISHISLYSLYS(chain A and (resid -2 through 0 or (resid 1...AA-2 - 3456 - 353
14HISHISLYSLYS(chain A and (resid -2 through 0 or (resid 1...AA-2 - 3456 - 353
15HISHISLYSLYS(chain A and (resid -2 through 0 or (resid 1...AA-2 - 3456 - 353
16HISHISLYSLYS(chain A and (resid -2 through 0 or (resid 1...AA-2 - 3456 - 353
21HISHISHISHIS(chain B and ((resid -2 through -1 and (name N...BB-2 - -16 - 7
22HISHISLYSLYS(chain B and ((resid -2 through -1 and (name N...BB-2 - 3456 - 353
23HISHISLYSLYS(chain B and ((resid -2 through -1 and (name N...BB-2 - 3456 - 353
24HISHISLYSLYS(chain B and ((resid -2 through -1 and (name N...BB-2 - 3456 - 353
25HISHISLYSLYS(chain B and ((resid -2 through -1 and (name N...BB-2 - 3456 - 353

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Components

#1: Protein Fructose-1,6-bisphosphate aldolase / Fructose-bisphosphate aldolase class 2 / Fructose-bisphosphate aldolase class II / Fructose- ...Fructose-bisphosphate aldolase class 2 / Fructose-bisphosphate aldolase class II / Fructose-bisphosphate aldolase / class II / Calvin cycle subtype


Mass: 38428.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: fbaA / Production host: Escherichia coli (E. coli) / References: UniProt: V5VDS0, fructose-bisphosphate aldolase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: AcbaC.01416.a.A1.PS02365 at 24 mg/mL against Morpheus G6 10% PEG 8000, 20% EG, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium potassium tartrate, 20 mM sodium oxamate, 0.1 M ...Details: AcbaC.01416.a.A1.PS02365 at 24 mg/mL against Morpheus G6 10% PEG 8000, 20% EG, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium potassium tartrate, 20 mM sodium oxamate, 0.1 M MOPS/Hepes pH 7.5, crystal ID 262645g6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→40.484 Å / Num. obs: 26739 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 6.669 % / Biso Wilson estimate: 46.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.079 / Χ2: 1.008 / Net I/σ(I): 16.15 / Num. measured all: 178325 / Scaling rejects: 7409
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.5-2.574.2740.4732.590.933181.4
2.57-2.644.7690.4682.90.949190.1
2.64-2.715.7490.3943.790.971195.6
2.71-2.86.9990.3335.130.983193.9
2.8-2.897.3810.2716.760.985193.7
2.89-2.997.3530.2268.190.986193.3
2.99-3.17.320.16610.30.993194.5
3.1-3.237.3180.15111.440.994194
3.23-3.377.280.11614.660.995195.1
3.37-3.547.1290.08619.260.997196.7
3.54-3.737.0220.07621.870.997197.5
3.73-3.956.9410.06724.240.997195.3
3.95-4.236.850.05726.770.998194.3
4.23-4.566.7730.05329.730.998196.6
4.56-56.8040.04531.820.998197.4
5-5.596.9850.04832.10.998198.2
5.59-6.467.1510.04632.370.999198.6
6.46-7.917.0430.04136.650.998198.3
7.91-11.186.9510.03241.750.999198.7
11.18-40.4846.8050.03641.980.997195.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.484 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 31.7
RfactorNum. reflection% reflection
Rfree0.2625 1352 5.06 %
Rwork0.1992 --
obs0.2024 26717 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.51 Å2 / Biso mean: 67.5301 Å2 / Biso min: 31.63 Å2
Refinement stepCycle: final / Resolution: 2.5→40.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 17 73 4914
Biso mean--62.9 53.64 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084936
X-RAY DIFFRACTIONf_angle_d0.9726727
X-RAY DIFFRACTIONf_chiral_restr0.058777
X-RAY DIFFRACTIONf_plane_restr0.007891
X-RAY DIFFRACTIONf_dihedral_angle_d13.4762934
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2749X-RAY DIFFRACTION10.5TORSIONAL
12B2749X-RAY DIFFRACTION10.5TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.58940.3361980.27562242234084
2.5894-2.69310.34381540.26022466262094
2.6931-2.81560.29631490.2712506265594
2.8156-2.9640.36361340.25832500263494
2.964-3.14970.33441320.24752541267394
3.1497-3.39280.33091390.24412542268195
3.3928-3.7340.25721640.20072584274898
3.734-4.27380.26541400.17712554269495
4.2738-5.38250.19891430.15622642278598
5.3825-40.48960.1916990.168227882887100
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)
13.0547-0.38471.13513.07292.00335.47090.2311-0.211-0.1706-0.0082-0.08720.0180.02640.2483-0.25390.3013-0.11910.00990.2865-0.00150.5352-14.0483-35.42544.5809
23.1778-0.04580.58351.5084-0.89442.13570.19090.20190.0643-0.0166-0.05390.2517-0.2331-0.1499-0.08090.34630.0334-0.01820.2892-0.08570.672-20.3761-26.1149-3.2291
34.73141.8404-2.22091.7751-1.36994.93840.15450.55080.2013-0.00040.02920.71920.2607-0.9072-0.16710.3576-0.0278-0.09110.3779-0.1250.744-35.6747-33.5973-2.4502
43.68370.3131-0.12891.7318-0.33181.14650.3563-0.7193-0.37830.3144-0.33950.31030.2285-0.1791-0.02510.4606-0.20970.05920.4402-0.03760.6337-24.6028-36.710112.1064
52.6061-1.45531.03231.5352-1.73252.26180.0325-0.15240.2893-0.044-0.1921-0.2789-0.008-0.1468-0.19060.4332-0.14470.0990.5146-0.26830.94256.4-2.636612.9899
61.75360.5346-0.31582.17030.78561.32520.1198-0.80710.5960.5504-0.26790.0183-0.17960.22390.15870.5398-0.21310.01130.673-0.16120.63276.206-13.943421.7742
70.26940.33610.80523.47051.79432.61410.1597-0.97310.78861.0436-0.46960.4009-0.1682-0.40050.21880.986-0.39790.01341.4405-0.60450.87035.8388-4.573237.5612
80.8754-0.16850.04781.14150.08431.286-0.1272-0.45590.36490.7271-0.1656-0.1363-0.0656-0.2485-0.56310.9848-0.50350.16291.4191-0.80430.607-4.5254-5.551733.7652
90.6136-0.29470.16460.52240.16370.59920.3453-0.73531.1560.3919-0.31270.1675-0.224-0.31590.07620.5925-0.2480.20050.7808-0.47121.0346-9.8305-9.466920.8085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 41 )A-2 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 135 )A42 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 202 )A136 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 345 )A203 - 345
5X-RAY DIFFRACTION5chain 'B' and (resid -2 through 15 )B-2 - 15
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 185 )B16 - 185
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 223 )B186 - 223
8X-RAY DIFFRACTION8chain 'B' and (resid 224 through 277 )B224 - 277
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 345 )B278 - 345

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