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- PDB-5u4n: Crystal structure of a fructose-bisphosphate aldolase from Neisse... -

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Basic information

Entry
Database: PDB / ID: 5u4n
TitleCrystal structure of a fructose-bisphosphate aldolase from Neisseria gonorrhoeae
ComponentsFructose-1
KeywordsLYASE / structural genomics / fructose / phosphate / 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 1. / 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
PHOSPHATE ION / Fructose-1,6-bisphosphate aldolase / Fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a fructose-bisphosphate aldolase from Neisseria gonorrhoeae
Authors: Edwards, T.E. / Horanyi, P.S. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionDec 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7375
Polymers39,3901
Non-polymers3474
Water6,143341
1
A: Fructose-1
hetero molecules

A: Fructose-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,47310
Polymers78,7792
Non-polymers6948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5880 Å2
ΔGint-69 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.950, 91.750, 85.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

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Components

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


Mass: 39389.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: fda, WHOF_00031C, WHOF_00393, WHOG_00032C, WHOG_01091, WHOK_00031C, WHOK_01288, WHOL_00032C, WHOL_00481, WHOM_00032C, WHOM_00338, WHON_00032C, WHON_00415, WHOO_00031C, WHOO_00479, WHOP_00030C, ...Gene: fda, WHOF_00031C, WHOF_00393, WHOG_00032C, WHOG_01091, WHOK_00031C, WHOK_01288, WHOL_00032C, WHOL_00481, WHOM_00032C, WHOM_00338, WHON_00032C, WHON_00415, WHOO_00031C, WHOO_00479, WHOP_00030C, WHOP_00448, WHOU_00032C, WHOU_01170, WHOV_00032C, WHOV_01444, WHOW_00031C, WHOW_01140, WHOX_00032C, WHOX_00360, WHOY_00032C, WHOY_00387, WHOZ_00031C, WHOZ_00311
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D3HPF5, UniProt: Q5FAI4*PLUS, fructose-bisphosphate aldolase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: NegoA.01416.a.PS37962 at 21.2 mg/mL against MCSG 1 screen condition G11 0.1 M phosphate citrate pH 4.2, 40% PEG 300, crystal tracking ID 282713a1, unique puck ID nce6-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→30.766 Å / Num. obs: 43174 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.788 % / Biso Wilson estimate: 13.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.36
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.6-1.645.330.5033.060.881199.5
1.64-1.696.6990.4464.050.9281100
1.69-1.747.4750.3835.030.9461100
1.74-1.798.2490.3156.450.9681100
1.79-1.858.2470.2388.410.9821100
1.85-1.918.2660.19110.450.9881100
1.91-1.988.2580.1513.330.9921100
1.98-2.078.2480.11617.170.9951100
2.07-2.168.2380.09420.660.9961100
2.16-2.268.2110.08123.860.9971100
2.26-2.398.20.0726.960.9981100
2.39-2.538.1950.06230.040.9981100
2.53-2.78.1430.05633.140.9981100
2.7-2.928.1160.04737.960.9991100
2.92-3.28.0560.04242.980.999199.9
3.2-3.588.0240.03549.580.999199.9
3.58-4.137.910.03253.240.999199.9
4.13-5.067.8820.02955.110.9991100
5.06-7.167.6830.02953.5511100
7.16-30.7666.8240.02752.450.999198.7

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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
Starting model: 3gay

3gay


Resolution: 1.6→30.766 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.93
RfactorNum. reflection% reflection
Rfree0.1754 1942 4.5 %
Rwork0.1457 --
obs0.147 43165 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.52 Å2 / Biso mean: 19.7443 Å2 / Biso min: 7.03 Å2
Refinement stepCycle: final / Resolution: 1.6→30.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 19 341 2978
Biso mean--25.67 33.61 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062747
X-RAY DIFFRACTIONf_angle_d0.7883746
X-RAY DIFFRACTIONf_chiral_restr0.055424
X-RAY DIFFRACTIONf_plane_restr0.005498
X-RAY DIFFRACTIONf_dihedral_angle_d14.4271667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.23231440.19722891303599
1.64-1.68430.21161640.174728693033100
1.6843-1.73390.2451150.170629433058100
1.7339-1.78990.19121260.162229353061100
1.7899-1.85380.18971390.153929083047100
1.8538-1.9280.18861410.149529263067100
1.928-2.01580.15411160.146229413057100
2.0158-2.1220.18911470.140429403087100
2.122-2.25490.19971460.14329053051100
2.2549-2.4290.18251480.142329403088100
2.429-2.67330.16981460.143429413087100
2.6733-3.05980.16821440.148229783122100
3.0598-3.85390.15521340.133229963130100
3.8539-30.77120.15011320.138731103242100
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)
13.16521.6743-1.09711.8062-0.90371.28960.0058-0.1097-0.07790.0276-0.0061-0.09940.0250.0302-0.00040.07150.0154-0.00820.0801-0.00460.074-9.5616-25.9153-6.5636
20.48680.3554-1.62731.3288-1.14785.8326-0.11860.0471-0.051-0.12560.0371-0.13890.268-0.07090.06330.0839-0.02280.00740.1053-0.00710.1312-6.1134-27.0807-17.2755
33.0235-0.52690.70180.9868-0.4040.9624-0.04550.1791-0.0235-0.13410.0128-0.02390.07050.04720.0290.1261-0.01010.00250.1134-0.02510.0806-22.3888-30.3299-18.5932
42.5036-1.4235-0.24743.29820.40062.00250.0710.1960.4199-0.1786-0.0345-0.1-0.2582-0.1428-0.05520.1127-0.0003-0.01050.13110.01230.1551-31.8192-19.5448-12.9471
51.48040.8496-0.60764.3658-0.97020.88970.1211-0.10730.22770.203-0.03810.1583-0.1657-0.0495-0.0960.09320.0021-0.010.1387-0.03060.0988-28.0319-14.2043-5.091
61.460.4671-0.67510.7261-0.3630.68250.0808-0.17940.23310.0602-0.00430.0208-0.09770.066-0.07440.1042-0.0079-0.00380.0925-0.04050.1032-9.4654-10.619-8.7305
73.55583.37052.9046.75863.32742.77080.418-0.3184-0.29460.4319-0.3426-0.00740.4966-0.11-0.11210.188-0.01350.0030.14830.04440.1275-15.7835-38.8115-3.5154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )A2 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 72 )A42 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 135 )A73 - 135
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 185 )A136 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 223 )A186 - 223
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 323 )A224 - 323
7X-RAY DIFFRACTION7chain 'A' and (resid 324 through 350 )A324 - 350

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