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- PDB-6vop: Crystal structure of YgbL, a putative aldolase/epimerase/decarbox... -

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Basic information

Entry
Database: PDB / ID: 6vop
TitleCrystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Escherichia coli
ComponentsAldolase
KeywordsLYASE / PUTATIVE LYASE / EPIMERASE / ALDOLASE / ISOMERASE / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES
Function / homology
Function and homology information


3-dehydro-4-phosphotetronate decarboxylase / L-fuculose-phosphate aldolase activity / pentose catabolic process / aldehyde-lyase activity / metal ion binding / cytosol
Similarity search - Function
: / : / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily
Similarity search - Domain/homology
3-oxo-tetronate 4-phosphate decarboxylase / 3-oxo-tetronate 4-phosphate decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support Canada, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C Canada
CitationJournal: To Be Published
Title: Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Escherichia coli
Authors: Stogios, P.J.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Aldolase


Theoretical massNumber of molelcules
Total (without water)23,1301
Polymers23,1301
Non-polymers00
Water99155
1
A: Aldolase

A: Aldolase

A: Aldolase

A: Aldolase


Theoretical massNumber of molelcules
Total (without water)92,5214
Polymers92,5214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area9530 Å2
ΔGint-37 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.796, 174.796, 174.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Space group name HallF423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x,y+1/2,z+1/2
#26: x,-z+1/2,y+1/2
#27: x,z+1/2,-y+1/2
#28: z,y+1/2,-x+1/2
#29: -z,y+1/2,x+1/2
#30: -y,x+1/2,z+1/2
#31: y,-x+1/2,z+1/2
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y,x+1/2,-z+1/2
#44: -y,-x+1/2,-z+1/2
#45: z,-y+1/2,x+1/2
#46: -z,-y+1/2,-x+1/2
#47: -x,z+1/2,y+1/2
#48: -x,-z+1/2,-y+1/2
#49: x+1/2,y,z+1/2
#50: x+1/2,-z,y+1/2
#51: x+1/2,z,-y+1/2
#52: z+1/2,y,-x+1/2
#53: -z+1/2,y,x+1/2
#54: -y+1/2,x,z+1/2
#55: y+1/2,-x,z+1/2
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+1/2,x,-z+1/2
#68: -y+1/2,-x,-z+1/2
#69: z+1/2,-y,x+1/2
#70: -z+1/2,-y,-x+1/2
#71: -x+1/2,z,y+1/2
#72: -x+1/2,-z,-y+1/2
#73: x+1/2,y+1/2,z
#74: x+1/2,-z+1/2,y
#75: x+1/2,z+1/2,-y
#76: z+1/2,y+1/2,-x
#77: -z+1/2,y+1/2,x
#78: -y+1/2,x+1/2,z
#79: y+1/2,-x+1/2,z
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+1/2,x+1/2,-z
#92: -y+1/2,-x+1/2,-z
#93: z+1/2,-y+1/2,x
#94: -z+1/2,-y+1/2,-x
#95: -x+1/2,z+1/2,y
#96: -x+1/2,-z+1/2,-y
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

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Components

#1: Protein Aldolase / Aldolase class II protein YgbL / Class II Aldolase and Adducin N-terminal domain protein / Class II ...Aldolase class II protein YgbL / Class II Aldolase and Adducin N-terminal domain protein / Class II aldolase / Epimerase/aldolase / Putative aldolase class 2 protein YgbL / Putative class II aldolase / Putative epimerase/aldolase / Ribulose-5-phosphate 4-epimerase / Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases


Mass: 23130.297 Da / Num. of mol.: 1 / Mutation: K78A, E79A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ygbL, fucA_1, fucA_2, fucA_3, A6V01_12630, A8C65_15140, A9R57_07175, AC789_1c30590, ACN002_2750, ACN68_01155, ACN81_22770, ACU57_10465, ACU90_22780, AM270_01140, AM446_07205, AM464_05380, AMK83_ ...Gene: ygbL, fucA_1, fucA_2, fucA_3, A6V01_12630, A8C65_15140, A9R57_07175, AC789_1c30590, ACN002_2750, ACN68_01155, ACN81_22770, ACU57_10465, ACU90_22780, AM270_01140, AM446_07205, AM464_05380, AMK83_11915, AML07_12225, APT94_21310, APZ14_09525, AUQ13_17325, AUS26_10160, AW106_00420, BANRA_01255, BANRA_03469, BANRA_03591, BANRA_04367, BB545_27775, BHS81_16420, BHS87_15520, BJJ90_05475, BK292_15630, BK334_27580, BK375_13210, BK383_11440, BMT91_16885, BN17_26181, BOH76_22435, BON63_19680, BON69_14795, BON71_18280, BON75_11965, BON76_10650, BON81_00285, BON83_09705, BON94_04140, BON95_16300, BTQ06_03125, BUE81_11725, BvCms12BK_03165, BvCms2454_01167, BvCms28BK_01877, BvCmsHHP001_03068, BvCmsHHP019_02729, BvCmsHHP056_03503, BvCmsKKP061_02297, BvCmsKSNP073_04251, BvCmsKSNP081_03742, BvCmsKSP011_03461, BvCmsKSP015_02034, BvCmsKSP024_00612, BvCmsKSP026_01128, BvCmsKSP045_01005, BvCmsKSP067_01661, BvCmsNSNP036_03000, BvCmsNSP006_05177, BvCmsNSP047_00861, BvCmsNSP072_00220, BvCmsOUP014_01965, BvCmsSINP011_00852, BvCmsSINP012_03946, BvCmsSIP019_02287, BvCmsSIP044_05163, BVL39_13210, BWI87_21825, BZL31_00610, C2U48_20265, C5N07_05940, C5P01_05225, C6669_14870, C7235_05990, C7B02_14785, C9025_10385, C9063_00245, C9077_06745, C9078_00240, C9083_12005, C9212_06240, C9299_06335, C9E25_03540, C9Y91_17090, C9Z12_17500, C9Z87_01290, CA593_13215, CG692_18935, CI641_006645, CI694_28410, COD30_02045, COD46_07295, CR538_05720, CRD98_12235, CRM83_26605, CRT46_16190, CWS33_18185, D2185_15215, D3821_16290, D3O91_08790, D3Y67_06215, D6W60_14495, D9D20_12755, D9D31_01300, D9D43_16575, D9E34_04445, D9G48_03345, D9H68_08840, D9H94_07975, D9I11_16525, D9I18_12570, D9I97_04710, D9J11_22615, D9J44_16120, D9K48_24075, DAH18_08020, DAH30_04920, DAH32_02260, DAH34_11955, DAH37_01550, DBQ99_06500, DD762_14650, DEN89_05940, DEN97_04175, DEO04_03140, DEO19_03955, DIV22_15765, DL545_06205, DL800_20265, DM102_17710, DNQ41_18745, DP277_11200, DQF57_14075, DQO13_13010, DS732_20470, DXT69_17430, DXT71_19600, DXT73_08290, E2119_10715, E2127_10915, E2128_08055, E2129_22655, E2134_08355, E2135_15730, E2855_03570, E2863_03416, E3B71_09995, E5P22_05820, E5P28_09955, E5S35_14170, E5S47_05195, EAI42_08185, EAI46_07305, EAI52_13045, EB575_07395, EC1094V2_959, EC3234A_48c00470, EC3426_03869, EC95NR1_01973, ECTO6_01118, ED600_08700, EEP23_04785, EHH55_21055, EIA08_26960, EJC75_12575, EKI52_20825, EL75_0949, EL79_0961, EL80_0963, ELT20_17290, ELV08_08120, ELV26_12010, ELV28_12625, EPS71_13390, EPS97_08775, EPT01_07465, EQ820_15255, EQ823_12350, ERS085365_02669, ERS085374_03154, ERS085379_00796, ERS085416_02009, ERS139211_02755, ERS150873_03405, ERS150876_01418, EXX24_16845, EXX71_08170, EXX78_11775, EYD11_05420, EYY19_02015, EYY78_17070, FAF34_024150, FNJ69_12040, FNJ79_10345, FORC28_1164, FORC82_1107, FQ915_18725, FQR64_05525, FRV13_23520, FTV93_24110, FV293_17575, FWK02_21690, HmCms184_04739, HmCmsJML074_00673, HmCmsJML079_02287, HW43_17945, NCTC10418_01757, NCTC10429_01799, NCTC10865_01414, NCTC11022_02815, NCTC11126_05115, NCTC11341_01131, NCTC13148_02634, NCTC8009_02569, NCTC8621_01097, NCTC8622_07110, NCTC8985_05864, NCTC9036_01185, NCTC9045_01263, NCTC9050_04116, NCTC9055_03095, NCTC9058_00801, NCTC9062_02092, NCTC9111_01568, NCTC9703_05685, NCTC9706_03345, PGD_04366, PU06_19290, RG28_07920, RK56_022935, RX35_01611, SAMEA3472043_01217, SAMEA3472044_02744, SAMEA3472047_00383, SAMEA3472055_01872, SAMEA3472070_01721, SAMEA3472080_02638, SAMEA3472114_04022, SAMEA3484427_01818, SAMEA3484429_01680, SAMEA3484434_01533, SAMEA3752553_01463, SAMEA3752557_03765, SAMEA3752559_03035, SAMEA3753064_03723, SAMEA3753097_02914, SAMEA3753290_03961, SK85_02974, UN86_26790, WQ89_15395, WR15_12820, YDC107_1288
Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold
References: UniProt: J7R4S3, UniProt: Q46890*PLUS, L-fuculose-phosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M Na Acetate pH 4.5, 3 M Na Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 7074 / % possible obs: 100 % / Redundancy: 29.6 % / Biso Wilson estimate: 42.02 Å2 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.049 / Net I/σ(I): 17.48
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 9 % / Rmerge(I) obs: 1.146 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 353 / CC1/2: 0.68 / Rpim(I) all: 0.389 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OPI

2opi


Resolution: 2.65→24.48 Å / SU ML: 0.4233 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2497
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 632 5.07 %RANDOM
Rwork0.1888 ---
obs0.1914 7033 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.63 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 0 55 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021616
X-RAY DIFFRACTIONf_angle_d0.47112196
X-RAY DIFFRACTIONf_chiral_restr0.0378249
X-RAY DIFFRACTIONf_plane_restr0.0038290
X-RAY DIFFRACTIONf_dihedral_angle_d23.4527599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.860.36231230.30482322X-RAY DIFFRACTION97.41
2.86-3.140.36311290.26452380X-RAY DIFFRACTION99.96
3.14-3.60.27591240.20212363X-RAY DIFFRACTION99.96
3.6-4.530.17111340.14332373X-RAY DIFFRACTION100
4.53-24.480.19521220.1562397X-RAY DIFFRACTION100
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)
14.22076544942.08412763286-5.184608838573.81827818171-2.373652774576.286868381940.246817454604-0.723592608027-0.265390303760.163642643303-0.171983264409-0.295963273117-0.4613496401871.06982501371-0.1641725544980.232482154512-0.0145216250661-0.03353193533150.4105194329380.005237855293120.31888739934258.5649146003-4.41694539167-15.3674391531
24.21899216126-3.4810184363-1.998602801627.560147017025.228148391994.20944100223-0.303554462541-0.0173282661944-0.1862381222140.6069100606110.159124156338-0.08369688234960.55017157927-0.1168068962840.1533040908110.3365930888-0.03264886844620.003502812722950.2667605566650.08765275099760.31237229257754.715757598-10.9648103498-17.2684994
38.39145453083-1.753691783774.077202334726.79806079135-4.307177066453.84886306945-0.122182391007-0.045796151501-0.336082571578-0.185305412623-0.120866294103-0.196380608574-0.7961671862560.09001358321790.2927125816310.3955868108920.03845912752430.01841744569740.3277576898630.04597917226430.38198490465356.6407529074-19.2798248648-25.377481073
44.52341708022-0.277077291127-1.716888893782.021316611441.594040704944.338966726990.1167317573950.4787358259660.0360584190203-0.233324791621-0.0229300540794-0.0281484094652-0.290250963011-0.284367379017-0.09485017627220.246042314843-0.00411259144628-0.03196579012470.246049969580.02115234620180.29551550749538.2584507549-5.7354303783-21.4586826622
53.06473406082-1.00785105697-1.582669640721.912073487310.3883856562443.056818872460.1453846780520.1937108456870.0421944863786-0.258282165106-0.09698856157470.0112319095567-0.169500762136-0.0816104947318-0.0509974472330.2508136786060.0118137624892-0.05243089261370.2960492006450.0411500864590.23914730145238.172270466-4.65849581894-21.129077971
66.20183004104-4.438689593550.106956281714.37881480758-1.546523242343.661099174330.3245561808390.494843698348-0.249675820529-0.06737788876280.2095034415660.892517805580.166983692182-1.8245636047-0.5116989138880.268445361859-0.02901334202710.009752731588910.450104213132-0.08881095831670.55080419692323.979442049610.0040982993-12.833803207
77.905493299093.182574199036.302050670168.80179364895-0.08343788208425.93819753703-0.3772828127732.01185437660.182383421094-1.1685956330.170928673664-0.5819181095050.1245013023471.882617687820.1360662590280.7658539751180.105519179222-0.1328768423920.673999924616-0.09322971072560.45274013184631.59200210413.722250488-27.2138627476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 212 )

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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