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- PDB-7ub8: The crystal structure of the K38A/K137A/K233A/K234A quadruple mut... -

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Basic information

Entry
Database: PDB / ID: 7ub8
TitleThe crystal structure of the K38A/K137A/K233A/K234A quadruple mutant of E. coli YGGS in complex with PLP
ComponentsPyridoxal phosphate homeostasis protein
KeywordsPROTEIN TRANSPORT / PLP-binding protein / Vitamin B6 / PLP homeostasis
Function / homologyUncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / PLP-binding barrel / pyridoxal phosphate binding / 1,4-BUTANEDIOL / PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate homeostasis protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDonkor, A.K. / Ghatge, M.S. / Musayev, F.N. / Safo, M.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129793 United States
Other governmentS10OD021756 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability.
Authors: Tramonti, A. / Ghatge, M.S. / Babor, J.T. / Musayev, F.N. / di Salvo, M.L. / Barile, A. / Colotti, G. / Giorgi, A. / Paredes, S.D. / Donkor, A.K. / Al Mughram, M.H. / de Crecy-Lagard, V. / ...Authors: Tramonti, A. / Ghatge, M.S. / Babor, J.T. / Musayev, F.N. / di Salvo, M.L. / Barile, A. / Colotti, G. / Giorgi, A. / Paredes, S.D. / Donkor, A.K. / Al Mughram, M.H. / de Crecy-Lagard, V. / Safo, M.K. / Contestabile, R.
History
DepositionMar 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Author supporting evidence / Database references / Structure summary
Category: audit_author / citation_author / pdbx_audit_support
Item: _citation_author.name
Revision 1.2Sep 28, 2022Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.5Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal phosphate homeostasis protein
B: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9417
Polymers51,1762
Non-polymers7655
Water3,405189
1
A: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0154
Polymers25,5881
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyridoxal phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9253
Polymers25,5881
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.646, 129.646, 76.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

21A-493-

HOH

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Components

#1: Protein Pyridoxal phosphate homeostasis protein / PLP homeostasis protein


Mass: 25588.035 Da / Num. of mol.: 2 / Mutation: K38A, K137A, K233A, K234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yggS, yggS_1, A5U30_002536, A6592_01605, A8499_002487, A9X72_04235, AAG43_002119, ABE90_008885, ACN81_19285, ACU57_02420, AM464_06455, APX88_16445, AT335_001847, AW119_01715, AWP93_03370, B6R31_ ...Gene: yggS, yggS_1, A5U30_002536, A6592_01605, A8499_002487, A9X72_04235, AAG43_002119, ABE90_008885, ACN81_19285, ACU57_02420, AM464_06455, APX88_16445, AT335_001847, AW119_01715, AWP93_03370, B6R31_003812, B6R48_004381, B6R87_004199, BANRA_03839, BANRA_04036, BF481_004825, BFL24_20630, BG944_003862, BGZ_03731, BHS81_17785, BIZ41_00110, BJI68_00120, BMC79_000896, BMT50_14985, BMT91_06560, BN17_28641, BO068_000828, BON63_07220, BON64_00505, BON66_18090, BON67_07075, BON68_25380, BON69_08055, BON71_16625, BON72_22075, BON73_20790, BON74_12080, BON75_05715, BON76_19600, BON77_06680, BON78_02935, BON79_04735, BON80_08660, BON84_07605, BON87_03690, BON88_27660, BON89_07800, BON90_06555, BON91_21215, BON92_03035, BON93_14700, BON94_11530, BON95_23425, BON96_08755, BON97_01525, BON98_24335, BR158_001158, BSR05_00525, BTQ06_15305, BvCmsF30A_00775, BvCmsHHP019_01430, BvCmsKKP036_00786, BvCmsKSNP073_01009, BvCmsNSP072_00005, BVL39_11960, C2121_000334, C2U48_19125, C3F40_21750, C5N07_11350, C5Y87_01815, C9114_13755, C9160_19505, C9E67_04785, CCS08_04675, CDC27_15720, CDL36_11990, CG692_04170, CG831_001596, CIG67_09495, CO706_12770, COD53_12020, CR538_04470, CR539_19790, CWS33_02090, CXJ73_003041, D3822_03980, D3G36_06505, D3Y67_09635, D9D77_01715, D9E34_07450, D9H94_01780, D9J61_17485, DAH19_03655, DAH20_07105, DAH21_16420, DAH22_01755, DAH23_02545, DAH24_02555, DAH25_06525, DAH26_02550, DAH27_13005, DAH28_14020, DAH29_07970, DAH30_03695, DAH31_07445, DAH32_08165, DAH33_07600, DAH36_04450, DAH38_14410, DAH40_03245, DAH41_08800, DAH42_03480, DAH43_04295, DAH45_02570, DAH46_04290, DAH47_01830, DAH48_00100, DAH49_05945, DAH50_00985, DEN87_23415, DEN88_15345, DEN89_15360, DEN90_09900, DEN93_01895, DEN94_02765, DEN95_05305, DEN96_03260, DEN97_02915, DEN98_02920, DEN99_00275, DEO00_02260, DEO01_06395, DEO02_04040, DEO03_09945, DEO04_01960, DEO05_01955, DEO06_10490, DEO07_10895, DEO08_05235, DEO09_01960, DEO10_03860, DEO11_03875, DEO12_19480, DEO13_03715, DEO14_14565, DEO15_02570, DEO17_09170, DEO18_08415, DEO19_02695, DEO20_04970, DIV22_04725, DM870_04190, DN627_06500, DNQ45_04905, DRW19_08955, DS732_21845, DTL43_08565, DTM16_23260, DTM45_03435, DU321_13160, DXT69_09050, DXT70_01070, DXT73_11060, E0I42_19975, E2113_22350, E2114_23105, E2115_25170, E2116_22045, E2117_06585, E2118_25780, E2119_17460, E2120_22990, E2121_10340, E2123_21170, E2124_21650, E2125_22595, E2127_08790, E2128_15520, E2129_10865, E2130_22720, E2132_07800, E2134_10685, E2136_04185, E5M02_18275, E5P22_07505, E5P23_16320, E5P24_19370, E5P25_09260, E5P30_04575, E5P31_12580, E5P32_10610, E5P35_01370, E5P36_03040, E5P37_15605, E5P39_18620, E5P40_16160, E5P41_17595, E5P42_03955, E5P43_17815, E5P44_03755, E5P45_15495, E5P46_17265, E5P47_15135, E5P48_16110, E5P49_09785, E5P50_06510, E5P51_14720, E5P52_04945, E5S34_19085, E5S35_06260, E5S36_16600, E5S37_19475, E5S38_02910, E5S39_05640, E5S42_02315, E5S43_06610, E5S44_08370, E5S46_03050, E5S47_04035, E5S48_19765, E5S51_01045, E5S52_07370, E5S53_08955, E5S55_07915, E5S56_10495, E5S57_01375, E5S58_01605, E5S61_06985, E5S62_00685, EA435_13755, EAI46_13050, EAN77_06340, EAX79_18760, EBP16_03495, EC3234A_50c00850, EC95NR1_02249, ECs3826, ED648_12865, EHD79_07725, EHH55_19850, EI021_05995, EIZ93_04705, EKI52_19505, EL79_0770, EL80_0765, ELT16_22100, ELT20_11815, ELT21_06930, ELT24_14260, ELT25_23905, ELT26_01120, ELT27_12075, ELT29_11660, ELT30_23070, ELT32_11085, ELT34_21400, ELT35_11005, ELT36_22555, ELT39_24285, ELT40_23250, ELT44_23345, ELT45_23015, ELT46_09740, ELT48_18535, ELT51_11245, ELT54_23985, ELT55_20860, ELT59_22130, ELT60_23295, ELT61_23190, ELT63_22530, ELT72_21945, ELU07_18210, ELU82_21625, ELU88_08890, ELU89_22125, ELU90_06760, ELU91_22220, ELU94_16485, ELU96_24085, ELU97_24105, ELU98_16800, ELV00_09650, ELV01_14635, ELV02_23710, ELV03_14355, ELV04_23130, ELV05_13450, ELV07_18185, ELV08_03735, ELV09_05255, ELV11_25160, ELV12_21430, ELV13_23925, ELV20_21495, ELV21_16555, ELV22_07885, ELV23_09990, ELV24_22210, ELV29_20480, ELX56_22225, ELX61_10855, ELX68_21270, ELX70_06600, ELX79_17745, ELX83_22385, ELX85_03700, ELY02_06930, ELY05_01540, ELY23_22015, ELY24_21105, ELY36_14265, ELY39_02230, ELY48_11860, ELY50_05765, EPS76_23030, ERS085406_01321, EVY14_04185, EXX13_15075, EYV17_01965, EYV18_21555, EYX47_12185, F0L67_07365, F2N31_22060, F7F11_00195, F9S76_07455, F9S83_14710, F9V24_03870, F9X20_25345, FE587_00885, FEJ01_00445, FFF58_11750, FJQ51_10270, FKO60_04535, FOI11_01810, FOI11_021370, FPI65_18190, FQ007_01470, FQF29_10150, FTV90_24115, FTV92_22795, FTV93_22815, FV293_10555, FVB16_24045, FY127_17985, FZN31_04490, G3565_13830, G5632_06490, G9448_18855, GIB53_14050, GKF86_09175, GKF89_08035, GKG12_00085, GNO40_18860, GNZ05_07955, GP650_01920, GP662_19735, GP946_14015, GP954_13245, GP979_21920, GQE64_15305, GQF59_22030, GQM04_18765, GQM09_03895, GQM13_07895, GQW68_13910, GQW80_01115, GRC73_21480, GRW05_17975, GRW57_26645, GRW81_17185, GTP88_07945, GUB08_20850, GUB92_14665, GUC01_11340, GUI33_09255, HHH44_003830, HI055_000095, HKA49_003353, HL563_05490, HLV18_01610, HLZ50_19300, HMU06_00730, HMU48_04490, HMV41_05740, HMV95_09385, HV209_16500, HV209_28430, HVV39_06655, HVW19_10795, HVW43_21550, HVX16_04630, HVX32_17080, HVY77_04590, HVZ71_04370, HX136_04100, I6H00_22940, I6H01_08680, I6H02_10245, IAI11_03475, IH768_06245, IH772_17565, IT029_002518, J0541_004081, J4S20_003608, J5U05_000108, JE86ST02C_34240, JE86ST05C_34280, JFD_01472, JNP96_22325, NCTC10082_03252, NCTC10089_00898, NCTC10090_03953, NCTC10418_01404, NCTC10429_01490, NCTC10865_01122, NCTC10958_00951, NCTC10974_01056, NCTC11126_04786, NCTC11181_03104, NCTC12950_01061, NCTC13148_02921, NCTC13216_00987, NCTC4450_02839, NCTC7928_01950, NCTC8008_00336, NCTC8009_02182, NCTC8179_06415, NCTC8333_00986, NCTC8450_05416, NCTC8959_02664, NCTC8985_05487, NCTC9036_00912, NCTC9037_01055, NCTC9045_01016, NCTC9111_01297, NCTC9117_01392, NCTC9775_04646, ND22_003843, RG28_06665, SAMEA3472044_02854, SAMEA3472067_03679, SAMEA3472080_03697, SAMEA3472147_01446, SAMEA3751407_00781, SAMEA3752557_03404, TUM18780_07680, WP2S18E08_09360, WP4S18E07_08580
Plasmid: pET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: C3SV52
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M Sodium acetate, pH 4.5,20% butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 11, 2021 / Details: VariMax TM-VHF Arc)Sec Confocal Optical System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.3→29.46 Å / Num. obs: 29721 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 25.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Net I/σ(I): 22 / Num. measured all: 396537 / Scaling rejects: 99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3813.60.3873902728630.9640.1070.4027.7100
8.91-29.4611.80.03169645880.9990.0090.0324697.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
CrysalisPro41.64.69adata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w8g

1w8g


Resolution: 2.3→29.105 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1496 5.04 %
Rwork0.1864 28161 -
obs0.1886 29657 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.64 Å2 / Biso mean: 26.1117 Å2 / Biso min: 7.95 Å2
Refinement stepCycle: final / Resolution: 2.3→29.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 48 189 3696
Biso mean--31.5 27.08 -
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3001-2.37430.25381440.20722499
2.3743-2.45910.2831260.22692531
2.4591-2.55750.27241420.20882508
2.5575-2.67380.23071410.21182513
2.6738-2.81470.28491410.20042517
2.8147-2.99080.25251440.20192524
2.9908-3.22150.23651300.20122557
3.2215-3.54520.2281140.19472572
3.5452-4.0570.23271250.17212602
4.057-5.10690.18541330.15352604
5.1069-29.1050.20371560.17022734

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