7TYE | pdb_00007tye

The crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase mutant (G108S) from E. Coli

PDB DOI: https://doi.org/10.2210/pdb7TYE/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-02-12 Released: 2022-02-23
Deposition Author(s): Tan, K., Perkovich, P., Joachimiak, A.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.224 (Depositor), 0.228 (DCC)
R-Value Work:
0.196 (Depositor), 0.199 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7TYE

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase mutant (G108S) from E. Coli

Tan, K., Perkovich, P., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 73.41 kDa
Atom Count: 4,870
Modeled Residue Count: 640
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3,4-dihydroxy-2-butanone 4-phosphate synthase	A, B, C	226	Escherichia coli	Mutation(s): 1 Gene Names: ribB, ribB_1, A6519_001821, A6583_08195, A6592_00475, A8C65_08565, A8W81_002595, A8X68_002370, A9819_17530, A9X72_03655... ribB, ribB_1, A6519_001821, A6583_08195, A6592_00475, A8C65_08565, A8W81_002595, A8X68_002370, A9819_17530, A9X72_03655, AAG43_000631, ABE90_004345, ABT96_003312, ACN68_04420, ACN81_21330, ACU57_05050, ACW72_002758, AM270_10855, AM340_10760, AM464_07470, AMK64_001824, AML23_19935, AO169_002970, APX88_18905, AT335_000760, AT845_001998, AUQ29_13020, AW059_22975, AW086_02310, B2D52_003328, B5N24_000792, B6L15_003047, B6R17_003588, B6R27_003447, B6R48_003723, B6R87_003495, B7C15_004686, BANRA_01658, BANRA_03956, BANRA_04051, BANRA_04205, BB545_10585, BE963_06040, BF271_001130, BF481_002801, BFL24_21180, BG821_002706, BG944_003509, BHF52_06970, BHS87_17190, BIQ87_17290, BJI68_02815, BJJ90_03530, BK292_10995, BK373_10875, BKD45_000386, BMC34_000332, BMC79_003295, BMT50_13620, BMT91_14570, BO068_000248, BOH76_02050, BON63_15045, BON65_07145, BON66_17455, BON70_12255, BON73_21300, BON76_06350, BON87_14390, BON93_10355, BON95_22875, BON96_07125, BTQ06_21170, BUE81_02910, BUE82_02710, BvCms2454_02340, BvCmsC61A_01364, BvCmsHHP019_01702, BvCmsHHP056_00960, BvCmsKKP005_04015, BvCmsKKP036_00383, BvCmsKKP057_00168, BvCmsKKP061_00971, BvCmsKSNP073_00205, BvCmsKSP011_03967, BvCmsKSP067_02749, BvCmsKSP076_01490, BvCmsNSNP036_02002, BvCmsSIP082_03546, BVL39_10960, BWI89_23105, BXT93_07215, C2M16_05000, C2U48_18630, C3F40_21225, C4952_000559, C5542_001780, C5715_01815, C5F72_04105, C5N07_16955, C5Y87_01265, C6B22_14795, C6N50_000045, C7B02_08385, C9114_14245, C9160_03115, C9E67_04240, C9Z62_01135, CA593_11110, CBT22_003186, CCS08_11265, CCZ91_002952, CDC27_16310, CDL36_05385, CF32_002004, CG692_20525, CG831_002556, CIG67_19720, CLG78_000376, CN875_002206, CO706_13820, COD50_12885, CR539_20275, CS116_002503, CV83915_03117, CWS33_20165, D0X26_08300, D3822_05205, D3O91_09960, D3Y67_11660, D5H22_00455, D6T60_20310, D9D77_02545, D9H13_08950, D9H94_02245, D9J03_01850, D9J11_00360, D9K17_10555, DAH18_13120, DAH23_16900, DAH34_16955, DAH37_03360, DAH50_01510, DB282_13640, DEN89_08565, DEN95_07415, DEO15_04205, DIV22_09975, DL654_14560, DLX40_00490, DM968_00310, DN627_00555, DNQ45_12580, DP258_07180, DRW19_00455, DS732_22790, DTL43_13415, DTL90_11885, DTM10_13585, DTM45_04080, DXT69_09580, DXT71_18690, DXT73_08665, E0I42_16405, E0N24_22480, E2112_15800, E2119_17625, E2127_16100, E2128_12480, E2129_12985, E2135_14860, E4K51_04755, E5P52_08445, E5S34_14980, E5S35_12445, E5S38_15370, E5S43_12575, E5S47_03535, E5S52_13245, E5S61_06420, E5S62_00060, EAX79_10065, EBP16_04025, EC1094V2_611, EC3234A_51c00960, EC95NR1_02415, ECs3929, ED648_05030, EGC08_05095, EH88_002433, EHD79_08380, EHH55_23580, EI021_05490, EI041_02750, EIA13_22925, EIZ93_03390, EKI52_19020, EL79_0666, EL80_0658, ELT21_11830, ELT31_13650, ELT49_09345, ELT58_01170, ELU85_07655, ELU95_11650, ELX69_05795, ELX76_20110, ELY05_21255, ELY48_00450, ERS085386_00632, ERS139208_02078, Esc0902E_33090, ETECE1373_00716, ETECE36_01331, ETECE925_00748, EVY14_08055, EXX13_07835, EXX79_06390, EYX47_17790, EYX55_17095, F2N27_05570, F2N28_04215, F2N31_03945, F3N40_23595, F9386_06745, F9400_13400, F9407_22160, F9S76_02440, F9S83_18085, F9V07_08290, F9V24_10835, F9X20_000585, F9X20_00575, FC554_17755, FDM60_11510, FFF58_12715, FHD44_03935, FHR00_18345, FJQ51_18915, FKO60_05520, FMP09_03755, FOI11_020545, FOI11_02635, FPS82_08210, FQ021_06460, FQE77_22590, FQF29_00510, FTV92_21975, FTV93_22170, FV293_12435, FY127_02275, FZC17_07490, FZN30_14545, G3813_002580, G4A38_09020, G5632_06905, G5696_02570, G6Z99_03325, G7635_002587, G9448_18360, GAJ26_00670, GBE29_13025, GF646_07945, GF699_06275, GFY34_05550, GFY48_06130, GFZ60_16630, GIB53_12220, GJ11_19995, GKF52_13910, GKF86_21645, GKF89_10300, GKG12_09310, GKZ24_21025, GNO40_18200, GNZ05_17920, GP650_03440, GP662_09035, GP946_07895, GP979_27370, GQE42_15525, GQE64_17785, GQE87_22865, GQF58_09845, GQF59_09985, GQM04_04665, GQM09_03395, GQM10_12705, GQM13_08705, GQR15_09500, GQW68_18060, GQW76_25445, GRQ19_14810, GRW05_30915, GRW05_30920, GRW57_06805, GRW57_20735, GRW80_00345, GRW81_06065, GSY44_06755, GUC01_10835, GXV26_002895, H0O72_14225, H4P47_03685, H4P50_03320, H4P51_03310, H5C78_19765, HCF72_000893, HHG09_005053, HHH44_002419, HIF90_001504, HIR12_002153, HIT56_000571, HJN04_002298, HJO75_003998, HJQ60_001955, HJS37_001886, HJS41_003640, HKA49_001389, HLU56_15610, HmCms184_01000, HMS79_13625, HMT08_03515, HMU48_02410, HMV95_05820, HNC30_10760, HNC36_03575, HNC52_11125, HNC59_18460, HNC75_05155, HNC99_14475, HNO08_12950, HNV65_01725, HNY50_02350, HPE39_22060, HV109_03480, HVV53_12470, HVW11_14015, HVX16_03705, HVX31_03065, HVY77_04050, HVZ29_17835, HVZ30_03155, HVZ33_03370, HX136_02895, HZ71_002968, I6H00_22190, I6H01_09465, I6H02_10780, IA00_001075, JE86ST02C_35250, JE86ST05C_35290, MJ49_15040, NCTC10082_03108, NCTC10090_03789, NCTC10429_01440, NCTC10764_04142, NCTC11022_03193, NCTC11181_02993, NCTC11341_01560, NCTC12950_00747, NCTC13148_03062, NCTC13216_01084, NCTC4450_02735, NCTC7922_03708, NCTC7927_00827, NCTC8008_05080, NCTC8179_06257, NCTC8500_00687, NCTC8622_07726, NCTC8960_03400, NCTC8985_05353, NCTC9036_00817, NCTC9045_00870, NCTC9048_00791, NCTC9050_03866, NCTC9073_05354, NCTC9077_00936, NCTC9111_01158, NCTC9117_01087, NCTC9702_00815, NCTC9703_05266, NCTC9706_03012, NCTC9777_02170, NCTC9962_00029, ND22_002317, PGD_04075, PU06_26310, RG28_20050, SAMEA3472043_01633, SAMEA3472044_01806, SAMEA3472056_04205, SAMEA3472064_00537, SAMEA3472080_00817, SAMEA3472112_02808, SAMEA3472117_03211, SAMEA3472147_02556, SAMEA3484427_04331, SAMEA3484429_04653, SAMEA3485101_01583, SAMEA3485110_00479, SAMEA3751407_00676, SAMEA3752312_02334, SAMEA3752386_00591, SAMEA3752557_02687, SAMEA3753064_03850, SAMEA3753290_04089, SAMEA3753300_03351, SM09_03329, THOESC010_07130, TUM18780_06690, UN91_14890, WP2S18E08_07400, WP4S18E07_06760, WP4S18E08_06750, WR15_10385 EC: 4.1.99.12
UniProt
Find proteins for P0A7J0 (Escherichia coli (strain K12)) Explore P0A7J0 Go to UniProtKB: P0A7J0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7J0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.224 (Depositor), 0.228 (DCC)
R-Value Work: 0.196 (Depositor), 0.199 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.99	α = 90
b = 108.514	β = 98.738
c = 47.438	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02- 06CH11357

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description