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- PDB-7k74: Crystal Structure of Fructose-1,6-bisphosphatase, type I, from St... -

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Basic information

Entry
Database: PDB / ID: 7k74
TitleCrystal Structure of Fructose-1,6-bisphosphatase, type I, from Stenotrophomonas maltophilia K279a
ComponentsFructose-1,6-bisphosphatase class 1
KeywordsHYDROLASE / SSGCID / Stenotrophomonas maltophilia K279a / Stenotrophomonas / Fructose-1 / 6-bisphosphatase / type I / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / magnesium ion binding / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
PHOSPHATE ION / Fructose-1,6-bisphosphatase class 1
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Fructose-1,6-bisphosphatase, type I, from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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-1,6-bisphosphatase class 1
B: Fructose-1,6-bisphosphatase class 1
C: Fructose-1,6-bisphosphatase class 1
D: Fructose-1,6-bisphosphatase class 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1258
Polymers149,7454
Non-polymers3804
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.040, 125.730, 158.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -2 through 9 or resid 11...
d_2ens_1(chain "B" and (resid -2 through 2 or (resid 3...
d_3ens_1(chain "C" and (resid -2 through 9 or resid 11...
d_4ens_1(chain "D" and (resid -2 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISGLNA1 - 12
d_12ens_1ALASERA14 - 79
d_13ens_1GLUASPA81 - 83
d_14ens_1SERTHRA85 - 127
d_15ens_1PROMETA130 - 233
d_16ens_1ALAPROA235 - 302
d_17ens_1PHEALAA304 - 324
d_18ens_1PO4PO4B
d_21ens_1HISGLNC1 - 12
d_22ens_1ALASERC14 - 79
d_23ens_1GLUASPC81 - 83
d_24ens_1SERTHRC85 - 127
d_25ens_1PROMETC130 - 233
d_26ens_1ALAPROC235 - 302
d_27ens_1PHEALAC304 - 324
d_28ens_1PO4PO4D
d_31ens_1HISGLNE1 - 12
d_32ens_1ALASERE14 - 79
d_33ens_1GLUASPE81 - 83
d_34ens_1SERMETE85 - 231
d_35ens_1ALAPROE233 - 300
d_36ens_1PHEALAE302 - 322
d_37ens_1PO4PO4F
d_41ens_1HISGLNG1 - 12
d_42ens_1ALASERG14 - 79
d_43ens_1GLUASPG81 - 83
d_44ens_1SERTHRG85 - 127
d_45ens_1PROMETG130 - 233
d_46ens_1ALAPROG235 - 302
d_47ens_1PHEALAG304 - 324
d_48ens_1PO4PO4H

NCS oper:
IDCodeMatrixVector
1given(-0.999993487985, -0.00352888920925, 0.000755597902004), (0.00353328144225, -0.999976395651, 0.00589271268789), (0.00073478533639, 0.00589534405451, 0.999982352349)0.0809907635088, 4.55708399178, -0.0358877967532
2given(-0.999999379296, -0.00104043645554, 0.000398622996494), (-0.00104450992551, 0.999945801818, -0.0103586883702), (-0.00038782383484, -0.0103590983062, -0.999946267894)-0.0145900643131, 0.000240698141186, -1.44540955647
3given(0.999973160254, 0.00692205349775, -0.00240082219581), (0.00690684479637, -0.999956388254, -0.0062862616516), (-0.00244423133122, 0.00626951082365, -0.999977359227)-0.0503860210916, 4.56246549495, -1.43196786979

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Components

#1: Protein
Fructose-1,6-bisphosphatase class 1 / FBPase class 1 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase class 1


Mass: 37436.363 Da / Num. of mol.: 4 / Fragment: StmaA.17936.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: fbp, Smlt0047 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FU10, fructose-bisphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents JCSG+ screen, condition h12: 45% (V/V) MPD, 200mM Ammonium acetate, 100mM HEPES free acid / NaOH pH 7.5: StmaA.17936.a.B1.PW38784 at 22.75mg/ml + 4mM fructose-1,6- ...Details: Rigaku Reagents JCSG+ screen, condition h12: 45% (V/V) MPD, 200mM Ammonium acetate, 100mM HEPES free acid / NaOH pH 7.5: StmaA.17936.a.B1.PW38784 at 22.75mg/ml + 4mM fructose-1,6-bisphosphate: tray: 315242h12, cryo: direct: puck: uog3-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 23, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 77671 / % possible obs: 99.7 % / Redundancy: 7.359 % / Biso Wilson estimate: 40.704 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.084 / Χ2: 0.868 / Net I/σ(I): 12.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.267.4740.5513.4556730.9710.59299.7
2.26-2.327.4690.4524.0255180.980.48599.7
2.32-2.397.4630.3744.6953760.9870.40299.6
2.39-2.467.460.3115.3152310.9910.33499.7
2.46-2.547.4680.272650750.9940.29299.6
2.54-2.637.4450.2127.0449260.9960.22899.7
2.63-2.737.4440.1688.447270.9970.18199.7
2.73-2.847.4420.1449.4945720.9970.15499.8
2.84-2.977.4260.12311.2343720.9980.13299.7
2.97-3.117.4050.09813.0942060.9980.10599.9
3.11-3.287.3480.08115.840280.9990.08799.7
3.28-3.487.310.06719.2738110.9980.07299.9
3.48-3.727.2720.0621.5635840.9980.06499.8
3.72-4.027.2170.05224.1233480.9990.05799.8
4.02-4.47.2090.04925.9530910.9990.05399.9
4.4-4.927.20.04327.8228120.9990.04799.9
4.92-5.687.1930.04426.125140.9990.04799.9
5.68-6.967.1210.0424.0921500.9990.043100
6.96-9.846.9630.03426.3516850.9990.03799.8
9.84-506.290.03326.239720.9990.03696.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1nuy as per Morda
Resolution: 2.2→37.78 Å / SU ML: 0.2585 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.9452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1973 2.57 %0
Rwork0.2135 74908 --
obs0.2145 76881 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9714 0 20 465 10199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00739999
X-RAY DIFFRACTIONf_angle_d0.881313604
X-RAY DIFFRACTIONf_chiral_restr0.0511525
X-RAY DIFFRACTIONf_plane_restr0.00831785
X-RAY DIFFRACTIONf_dihedral_angle_d12.93533543
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.298195496229
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.265826502606
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.30968365196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.35851350.27245289X-RAY DIFFRACTION98.98
2.26-2.320.29191430.26085280X-RAY DIFFRACTION98.98
2.32-2.380.31281300.25165293X-RAY DIFFRACTION98.58
2.38-2.460.28391670.24575244X-RAY DIFFRACTION98.54
2.46-2.550.28911420.23115302X-RAY DIFFRACTION98.66
2.55-2.650.29031270.23275274X-RAY DIFFRACTION98.41
2.65-2.770.31861530.22615280X-RAY DIFFRACTION98.26
2.77-2.920.26181410.24175324X-RAY DIFFRACTION98.91
2.92-3.10.32291470.23235326X-RAY DIFFRACTION99.24
3.1-3.340.23351240.22125418X-RAY DIFFRACTION99.41
3.34-3.680.22731380.19815399X-RAY DIFFRACTION99.3
3.68-4.210.19381440.18235437X-RAY DIFFRACTION99.66
4.21-5.30.21741420.17745471X-RAY DIFFRACTION99.57
5.3-37.780.2361400.21925571X-RAY DIFFRACTION97.01
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0096798614-0.9918450024890.5033769728857.77734391495-2.575542023282.926849787950.384086418591-0.0589266348379-0.7201769597960.683137137173-0.155169054173-1.140895525480.09979380707610.494984155162-0.3007260024920.662137976060.0330608174287-0.1842018867840.9356425877250.02228055541950.88556591092313.3728437054-10.0148543896-13.4285393768
20.614517809613-0.579166339839-0.3488360215861.56427045183-0.4727238035126.070463381240.30367260092-0.1648050521390.009148714757460.2181253887880.0968538781106-0.2807281468080.8432247283031.17396028206-0.2984373844680.6244037163650.150860599307-0.2020272093630.66890274453-0.0892970911920.6123640708359.49429015819-25.0463368747-12.0677424895
31.202095799750.1944259864170.06848327361541.385727389120.04286372427811.884163474510.1494978680380.135917511248-0.1551087059180.10852536576-0.018082761155-0.04986805144220.289122453727-0.0726268812601-0.1278900055430.282906988544-0.0238214877846-0.06545197583970.294780137346-0.05517470156280.303205551593-3.00081652781-10.0777004616-27.5957135493
41.38110583857-0.2871240976980.4503467193161.77594093037-0.8407543925912.896883645610.1514721614310.424395051791-0.3222477193670.0010378173212-0.0266701849804-0.0731540426660.5524576880280.213427300259-0.1219004383660.3367362594980.0179529852392-0.09514093620950.345556564094-0.1479312872240.351177153467-2.70172256599-18.2106508578-35.9631474345
54.672395657714.232110148060.7201098127047.201249221970.8421935368312.454885451670.337143357357-0.2958540705410.1484581220750.863953040733-0.199033407303-0.103519151999-0.184136630144-0.0257021717868-0.1126668077870.369358538952-0.04987582970250.06712173693660.220010859916-0.01240770767880.2737280714674.1902692329320.4476539167-8.60571590651
61.047744281760.736330675011.207200991945.559040834954.032447354193.367382743570.09321514652370.4429850349570.3316864418120.553254333359-0.4579107675881.235899926590.445143018207-0.5626509773690.332441128240.5023103866150.02196928831250.1320298878920.663645162889-0.06024878274920.670336415309-11.788183409217.2519447073-11.0334169424
73.92266685946-0.4741083317830.6368252388082.60005170180.3912558880134.499037575460.0751906206031-0.7421276831210.06034050245540.482780951549-0.3402555469010.539356804689-0.498345089613-0.7600878034910.3518266225440.4840539281960.09070158386580.1547139745820.467159040350.02769437242310.54793737459-10.604028928929.8852125591-14.6315825975
81.301347151380.08632733484940.3993268138771.132019092490.6038627462391.962187036140.07542730731960.1525853019410.1480794428770.0566460500307-0.0118102070120.021514437041-0.1151339980590.0548251292431-0.06501472318530.250695998096-0.04235653105580.04949582677050.261240865640.03172959691440.2841289099082.3337650081816.1290226409-25.1973946757
91.131574795950.0121650221464-0.2458588327712.07734734270.5442788296072.36197345430.08350956602840.3757530811490.253050333119-0.221223033072-0.01601540293070.0863257176467-0.370500178255-0.0630764577201-0.07106861484090.2443959702180.00384166836090.03439747178550.3281843413370.08837293729250.274755985892.8723652521117.5200944437-35.8130852685
102.4950956131-2.560561224270.5740538691237.3751230767-1.054312294743.769608171790.2198328324340.178534651174-0.215246291609-0.769966407451-0.121408452523-0.1036501163680.4446534313590.207830285785-0.09103980760940.4591783729830.0177898574774-0.06292638800170.33027532679-0.04962241240410.298252151184.0727111417-15.65286390566.99055269906
113.60912465107-1.15893541324-1.101544865487.118850393261.872045428433.478276736960.6301332076570.267686970479-0.592262460883-0.377384208844-0.3823614180021.335974676840.175471838954-0.00987979483392-0.182292117230.632532319976-0.12638468678-0.2052985398820.9589609928430.05156162668641.02927263785-13.4042499337-10.205194375612.3028557075
121.56335821120.560207705182-0.5719406413771.709847110760.9029717336024.590505301890.3528252069960.154603064456-0.0204221037644-0.330029153586-0.05345039943160.1232257149950.652872079594-0.737916973275-0.2460674763550.700996949997-0.19049465479-0.1873399299860.5550567232770.06861445508540.639898503394-9.50619833969-24.943542799410.8955433406
131.0519877982-0.0398115532244-0.100104179151.46152718614-0.00920419885942.170752736140.123832565159-0.141096793738-0.2651677396630.0338902071154-0.1234046121320.4033550079070.521998674399-0.04268570019870.0008703877173060.42478478635-0.0200545646662-0.06533453628030.3091263772380.03947238691040.395026290358-3.30268629216-18.257131310319.3197064829
141.07217237116-0.236020434638-0.5555424544871.232271032970.003292049435013.773349722140.0659870796209-0.225649470573-0.061864482581-0.008190036563870.0180103932895-0.04739005359470.1574495309070.149203091255-0.09782759839810.181662649547-0.0237687389923-0.04514584879420.2717790260520.04095983737770.2348857978235.93316843326-6.0792048361129.3729035978
151.31958145673-0.3861565000060.4936475788442.017936541490.5227255139893.775293141810.0419594534059-0.396484951749-0.2492320113550.02916861710390.02021766717310.1315158944190.558325542549-0.117784438064-0.04828488744180.311990096437-0.0597455511507-0.04508130026180.3643516106690.1417622247130.3221868075142.68448253278-17.821850052434.6818643559
165.33776983035-4.798478745850.820211032825.77403922609-0.6249435622862.703672891820.3295051641150.358258971158-0.0838171722885-0.637576406903-0.1919840554450.16808748211-0.200351900101-0.0448284870534-0.1370215329620.3272912198030.00502905171880.04799626193370.2131218129190.02339333898820.249542868392-4.5987602426620.66554335176.71372683247
172.918247350460.532651021306-0.6223984934176.2800491511-2.749021668653.561165635320.536221002918-0.3772237028120.430577863784-0.162336985939-0.322244365648-0.826588700661-0.2672767388020.19608953611-0.1979743133620.603527095167-0.1175548223850.1285788957060.7562684086680.009681987181580.71919612277813.28624572714.326773471512.112593003
182.2431612060.3339222580180.9658137362130.9311630141620.6562181350692.83088364206-0.06200639161820.243442403592-0.0600192513889-0.436728368470.0430584160862-0.32323993849-0.4852018843340.4880546975980.06095691986230.568035742758-0.2127725818840.1568875751980.548838044282-0.04281437056650.5384932188559.6467145750129.532584844210.6519434701
191.23522978243-0.0109309013615-0.1821132868431.15044577615-0.5294439531422.353405521640.0927248724202-0.2697243405050.1838096247040.0594655293587-0.0277170212577-0.0643868003664-0.2618289494910.0742946151082-0.05305366043550.235750727622-0.05517936326910.03630499466190.261954551488-0.05128632365410.274683857558-2.6466572310117.134822899228.6691376332
202.981087234812.230287755640.02426697547957.56723460463-0.988657398093.334650504360.358035828737-0.184437750963-0.229060375850.803378254492-0.1565104018270.1338413754610.517680370728-0.180806915131-0.1548709362040.426989484866-0.0865559082861-0.07104004157750.2848040639310.04038664213740.27901586553-4.25627000111-15.9332590436-8.30675966387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 42 through 70 )CE42 - 7045 - 65
22chain 'C' and (resid 71 through 101 )CE71 - 10166 - 96
33chain 'C' and (resid 102 through 262 )CE102 - 26297 - 253
44chain 'C' and (resid 263 through 331 )CE263 - 331254 - 322
55chain 'D' and (resid -2 through 41 )DG-2 - 411 - 44
66chain 'D' and (resid 42 through 75 )DG42 - 7545 - 70
77chain 'D' and (resid 76 through 101 )DG76 - 10171 - 96
88chain 'D' and (resid 102 through 225 )DG102 - 22597 - 218
99chain 'D' and (resid 226 through 331 )DG226 - 331219 - 324
1010chain 'A' and (resid -2 through 42 )AA-2 - 421 - 45
1111chain 'A' and (resid 43 through 70 )AA43 - 7046 - 65
1212chain 'A' and (resid 71 through 101 )AA71 - 10166 - 96
1313chain 'A' and (resid 102 through 157 )AA102 - 15797 - 150
1414chain 'A' and (resid 158 through 262 )AA158 - 262151 - 255
1515chain 'A' and (resid 263 through 331 )AA263 - 331256 - 324
1616chain 'B' and (resid -2 through 41 )BC-2 - 411 - 44
1717chain 'B' and (resid 42 through 70 )BC42 - 7045 - 65
1818chain 'B' and (resid 71 through 101 )BC71 - 10166 - 96
1919chain 'B' and (resid 102 through 331 )BC102 - 33197 - 324
2020chain 'C' and (resid -2 through 41 )CE-2 - 411 - 44

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