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- PDB-3qm3: 1.85 Angstrom Resolution Crystal Structure of Fructose-bisphospha... -

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Basic information

Entry
Database: PDB / ID: 3qm3
Title1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from Campylobacter jejuni
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM beta/alpha-barrel
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, yeast/E. coli subtype / 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
FORMIC ACID / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from Campylobacter jejuni
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_label_asym_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.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

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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
E: Fructose-bisphosphate aldolase
F: Fructose-bisphosphate aldolase
G: Fructose-bisphosphate aldolase
H: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,65148
Polymers312,3848
Non-polymers3,26740
Water64,1693562
1
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,93712
Polymers78,0962
Non-polymers84110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-179 kcal/mol
Surface area26740 Å2
MethodPISA
2
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,92713
Polymers78,0962
Non-polymers83111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-192 kcal/mol
Surface area25970 Å2
MethodPISA
3
E: Fructose-bisphosphate aldolase
F: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,93712
Polymers78,0962
Non-polymers84110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-175 kcal/mol
Surface area26630 Å2
MethodPISA
4
G: Fructose-bisphosphate aldolase
H: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,84911
Polymers78,0962
Non-polymers7539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-191 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.996, 101.971, 105.662
Angle α, β, γ (deg.)113.27, 95.34, 95.75
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Fructose-bisphosphate aldolase / / FBP aldolase / FBPA / Fructose-1 / 6-bisphosphate aldolase


Mass: 39048.020 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: Cj0597, fba, fda, fdaC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRXpGro7 / References: UniProt: Q0PAS0, fructose-bisphosphate aldolase

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Non-polymers , 6 types, 3602 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3562 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5) Screen solution: 0.2M NH4 Sulfate, 0.1M Na Cacodylate pH 7.5, 30%PEG 2K MME, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2010 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 242214 / Num. obs: 242214 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 21
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.7 / Num. unique all: 12007 / % possible all: 96.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOS

1dos


Resolution: 1.85→29.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.314 / SU ML: 0.074
Isotropic thermal model: Atomic Temperature Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19088 12186 5 %RANDOM
Rwork0.14888 ---
all0.15097 229995 --
obs0.15097 229995 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.314 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0.67 Å2-0.2 Å2
2--0.64 Å20.98 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21314 0 159 3562 25035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02222243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214875
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.96630090
X-RAY DIFFRACTIONr_angle_other_deg0.844336627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.97452828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63625.853991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.538153905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0651556
X-RAY DIFFRACTIONr_chiral_restr0.0890.23281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024156
X-RAY DIFFRACTIONr_mcbond_it0.9891.513919
X-RAY DIFFRACTIONr_mcbond_other0.3421.55774
X-RAY DIFFRACTIONr_mcangle_it1.618222277
X-RAY DIFFRACTIONr_scbond_it2.80838324
X-RAY DIFFRACTIONr_scangle_it4.3424.57812
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 900 -
Rwork0.203 16469 -
obs-16469 94.81 %
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)
10.60610.1222-0.14430.74710.04020.3260.025-0.05550.00910.1163-0.0439-0.0111-0.01170.0310.01890.0513-0.0142-0.00780.0349-0.00840.007255.975847.5155104.3828
21.15310.4951-0.36341.4033-0.4951.39490.05590.06140.2265-0.01330.01780.0678-0.08620.0011-0.07370.0377-0.01070.01040.0267-0.0030.060455.327865.976896.6642
30.31-0.0726-0.11091.45960.25360.2056-0.0060.0727-0.0171-0.03940.037-0.13140.0250.0184-0.0310.0123-0.0024-0.00020.042-0.0120.015768.304235.773386.728
41.23310.25410.16421.0903-0.18450.91670.0389-0.1045-0.20990.1338-0.0551-0.06280.06640.02690.01620.03830.0012-0.00230.02180.02070.038557.222915.3429108.1249
52.67810.27680.84561.75740.29422.82140.16710.0953-0.6987-0.062-0.0525-0.11370.49120.0856-0.11460.17450.0147-0.01380.01790.00780.269856.1855-2.5284105.1323
60.7920.487-0.41320.8464-0.30670.7769-0.07510.18360.0169-0.18660.10190.07420.0229-0.0946-0.02680.0472-0.0058-0.02150.0752-0.01170.018353.79527.933583.1833
70.68850.12110.07810.9559-0.0390.468-0.0009-0.03840.01650.06410.0138-0.021-0.01590.0135-0.01290.0150.0058-0.00680.032-0.0210.014771.698816.353755.672
80.93770.1935-0.27071.1301-0.33590.6825-0.00690.09750.1906-0.00950.07580.0948-0.0599-0.0671-0.06890.02470.0052-0.01780.0446-0.00580.07862.210532.639151.1055
90.28980.0227-0.0260.88660.26520.2876-0.00020.0561-0.0115-0.03550.0314-0.0950.02790.0367-0.03120.01730.0027-0.00140.0437-0.02030.022578.37846.135939.5618
100.85660.28270.13290.7830.00160.70580.0099-0.1201-0.05280.05790.00230.05750.0459-0.0637-0.01220.02180.0004-0.00190.04090.00360.018261.4646-8.916558.1635
111.06340.63190.56352.4191-0.43561.8760.098-0.0537-0.22790.0123-0.063-0.24370.2920.1158-0.0350.0780.0253-0.01920.04550.03180.067870.333-24.282864.9636
120.31370.1913-0.20170.5641-0.35710.9746-0.02750.0565-0.0239-0.11350.06020.03320.0825-0.0697-0.03260.0279-0.0015-0.01590.0417-0.02210.023163.2805-5.832438.6646
130.9507-0.33580.06351.0729-0.03380.29780.07590.1024-0.0751-0.1026-0.07320.07970.05330.0409-0.00270.02710.0344-0.01020.0822-0.01280.009126.8408-4.968335.2344
141.9898-0.9457-0.18122.7155-0.63542.01610.0128-0.1111-0.20340.16420.02850.07930.07510.0679-0.04130.03290.0297-0.00640.08850.0040.055831.4272-18.194445.1036
150.4362-0.17420.07411.2990.14650.3212-0.011-0.03490.0850.10690.0052-0.1278-0.00930.05630.00590.01260.002-0.01290.09090.010.03839.745412.731649.9849
160.6692-0.3896-0.40311.2316-0.36491.28630.1170.08790.1944-0.1265-0.1002-0.1586-0.18860.0798-0.01680.0582-0.00820.02090.09720.0560.092627.849336.80826.803
175.3017-1.3554-3.1614.39150.41641.94850.2823-0.70940.37370.498-0.0684-0.2887-0.30730.4739-0.2140.3507-0.0959-0.00940.2718-0.00370.198923.672245.789739.4183
180.5808-0.33380.4660.9119-0.15880.9844-0.0297-0.06840.04790.2450.02390.03070.0089-0.04180.00580.0749-0.01370.01550.1290.00590.053925.361520.768453.2033
190.5614-0.17750.11040.6262-0.08360.24160.00350.0476-0.0173-0.084-0.01230.04030.0410.0280.00880.02910.0006-0.00050.0247-0.01380.013917.213528.574280.6433
201.5086-0.46570.0292.19-0.34481.67010.0034-0.1062-0.28030.03320.08410.11820.14190.0058-0.08750.02950.00550.00120.02350.00620.077717.83079.899689.885
210.424-0.06760.01921.16030.19240.2909-0.0111-0.07920.05190.07460.0157-0.0845-0.03180.0377-0.00460.0154-0.0002-0.00920.0349-0.01590.015229.64541.336298.334
220.9776-0.4206-0.0641.4729-0.05990.84270.06440.10610.1296-0.1037-0.05320.0705-0.0611-0.05-0.01120.01860.00440.00090.02130.01270.0313.062857.751880.4686
232.1063-0.6801-0.99041.9340.04221.96450.27840.09380.5678-0.1246-0.0928-0.348-0.33750.0729-0.18550.1147-0.0180.07030.04360.06980.22121.827573.373775.4641
240.6227-0.49440.20671.2341-0.38640.844-0.0373-0.10610.0620.20790.06490.056-0.0409-0.038-0.02760.0469-0.01010.02270.0462-0.02860.034614.849252.0399100.1371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 157
2X-RAY DIFFRACTION2A158 - 266
3X-RAY DIFFRACTION3A267 - 354
4X-RAY DIFFRACTION4B0 - 188
5X-RAY DIFFRACTION5B189 - 281
6X-RAY DIFFRACTION6B282 - 354
7X-RAY DIFFRACTION7C0 - 104
8X-RAY DIFFRACTION8C105 - 266
9X-RAY DIFFRACTION9C267 - 354
10X-RAY DIFFRACTION10D0 - 104
11X-RAY DIFFRACTION11D105 - 266
12X-RAY DIFFRACTION12D267 - 354
13X-RAY DIFFRACTION13E0 - 220
14X-RAY DIFFRACTION14E221 - 266
15X-RAY DIFFRACTION15E267 - 354
16X-RAY DIFFRACTION16F-2 - 260
17X-RAY DIFFRACTION17F261 - 282
18X-RAY DIFFRACTION18F283 - 354
19X-RAY DIFFRACTION19G0 - 174
20X-RAY DIFFRACTION20G175 - 266
21X-RAY DIFFRACTION21G267 - 354
22X-RAY DIFFRACTION22H0 - 104
23X-RAY DIFFRACTION23H105 - 270
24X-RAY DIFFRACTION24H271 - 354

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