6VOP | pdb_00006vop

Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb6VOP/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-01-31 Released: 2020-02-19 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Escherichia coli

Stogios, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.13 kDa 
• Atom Count: 1,640 
• Modeled Residue Count: 207 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldolase	A	212	Escherichia coli	Mutation(s): 2  Gene Names:  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 EC: 4.1.2.17 (PDB Primary Data), 4.1.1.104 (UniProt)
UniProt
Find proteins for Q46890 (Escherichia coli (strain K12)) Explore Q46890  Go to UniProtKB:  Q46890

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.796	α = 90
b = 174.796	β = 90
c = 174.796	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	Canada	HHSN272201700060C

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description