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- PDB-7vza: The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in... -

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Basic information

Entry
Database: PDB / ID: 7vza
TitleThe crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP
ComponentsPutative UDP-N-acetylglucosamine 2-epimerase
KeywordsISOMERASE / Epimerase / UDP-sugars
Function / homologyUDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)
Function and homology information
Biological speciesStreptomyces kasugaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLi, T.L. / Rattinam, R.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Biomedicines / Year: 2022
Title: KasQ an Epimerase Primes the Biosynthesis of Aminoglycoside Antibiotic Kasugamycin and KasF/H Acetyltransferases Inactivate Its Activity.
Authors: Rattinam, R. / Basha, R.S. / Wang, Y.L. / Wang, Z.C. / Hsu, N.S. / Lin, K.H. / Zadeh, S.M. / Adhikari, K. / Lin, J.P. / Li, T.L.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Refinement description / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct_ncs_dom_lim
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Putative UDP-N-acetylglucosamine 2-epimerase
B: Putative UDP-N-acetylglucosamine 2-epimerase
C: Putative UDP-N-acetylglucosamine 2-epimerase
D: Putative UDP-N-acetylglucosamine 2-epimerase
E: Putative UDP-N-acetylglucosamine 2-epimerase
F: Putative UDP-N-acetylglucosamine 2-epimerase
G: Putative UDP-N-acetylglucosamine 2-epimerase
H: Putative UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,08324
Polymers329,6668
Non-polymers3,41716
Water6,017334
1
A: Putative UDP-N-acetylglucosamine 2-epimerase
B: Putative UDP-N-acetylglucosamine 2-epimerase
G: Putative UDP-N-acetylglucosamine 2-epimerase
hetero molecules

C: Putative UDP-N-acetylglucosamine 2-epimerase
E: Putative UDP-N-acetylglucosamine 2-epimerase
hetero molecules

D: Putative UDP-N-acetylglucosamine 2-epimerase
hetero molecules

F: Putative UDP-N-acetylglucosamine 2-epimerase
H: Putative UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,08324
Polymers329,6668
Non-polymers3,41716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_456x-1,y,z+11
crystal symmetry operation1_545x,y-1,z1
Buried area30110 Å2
ΔGint-239 kcal/mol
Surface area101420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.820, 104.770, 106.314
Angle α, β, γ (deg.)74.536, 73.051, 68.390
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74A
84E
95A
105F
116A
126G
137A
147H
158B
168C
179B
189D
1910B
2010E
2111B
2211F
2312B
2412G
2513B
2613H
2714C
2814D
2915C
3015E
3116C
3216F
3317C
3417G
3518C
3618H
3719D
3819E
3920D
4020F
4121D
4221G
4322D
4422H
4523E
4623F
4724E
4824G
4925E
5025H
5126F
5226G
5327F
5427H
5528G
5628H

NCS domain segments:

Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 0 - 374 / Label seq-ID: 1 - 375

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
221BB
332AA
442CC
553AA
663DD
774AA
884EE
995AA
10105FF
11116AA
12126GG
13137AA
14147HH
15158BB
16168CC
17179BB
18189DD
191910BB
202010EE
212111BB
222211FF
232312BB
242412GG
252513BB
262613HH
272714CC
282814DD
292915CC
303015EE
313116CC
323216FF
333317CC
343417GG
353518CC
363618HH
373719DD
383819EE
393920DD
404020FF
414121DD
424221GG
434322DD
444422HH
454523EE
464623FF
474724EE
484824GG
494925EE
505025HH
515126FF
525226GG
535327FF
545427HH
555528GG
565628HH

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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Components

#1: Protein
Putative UDP-N-acetylglucosamine 2-epimerase


Mass: 41208.227 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kasugaensis (bacteria) / Gene: kasQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1H2R6
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate, 0.1M Bis tris pH5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→19.895 Å / Num. obs: 91395 / % possible obs: 94.1 % / Redundancy: 2.4 % / Rrim(I) all: 0.05 / Net I/σ(I): 23.8
Reflection shellResolution: 2.6→2.68 Å / Num. unique obs: 91395 / Rrim(I) all: 0.05

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGV
Resolution: 2.58→19.895 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.897 / SU B: 13.216 / SU ML: 0.271 / Cross valid method: NONE / ESU R Free: 0.341
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2488 4644 5.081 %
Rwork0.2098 86751 -
all0.212 --
obs-91395 93.946 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.417 Å2-0.312 Å20.101 Å2
2---0.371 Å20.044 Å2
3----0.098 Å2
Refinement stepCycle: LAST / Resolution: 2.58→19.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22203 0 208 334 22745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01322791
X-RAY DIFFRACTIONr_bond_other_d0.0010.01722167
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6630982
X-RAY DIFFRACTIONr_angle_other_deg1.181.57850781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46852848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58219.4051310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.815153732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.64915293
X-RAY DIFFRACTIONr_chiral_restr0.0610.22983
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025189
X-RAY DIFFRACTIONr_nbd_refined0.1950.24444
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.220281
X-RAY DIFFRACTIONr_nbtor_refined0.1460.210798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.211222
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2533
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.27
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.293
X-RAY DIFFRACTIONr_nbd_other0.2150.2323
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.220
X-RAY DIFFRACTIONr_mcbond_it3.3624.57311494
X-RAY DIFFRACTIONr_mcbond_other3.3624.57311493
X-RAY DIFFRACTIONr_mcangle_it5.1856.84914308
X-RAY DIFFRACTIONr_mcangle_other5.1856.8514309
X-RAY DIFFRACTIONr_scbond_it3.6245.06811297
X-RAY DIFFRACTIONr_scbond_other3.6245.06911296
X-RAY DIFFRACTIONr_scangle_it5.8457.41716674
X-RAY DIFFRACTIONr_scangle_other5.8447.41716675
X-RAY DIFFRACTIONr_lrange_it8.39953.54123588
X-RAY DIFFRACTIONr_lrange_other8.453.5523558
X-RAY DIFFRACTIONr_ncsr_local_group_10.0610.0511165
X-RAY DIFFRACTIONr_ncsr_local_group_20.0670.0511008
X-RAY DIFFRACTIONr_ncsr_local_group_30.0570.0511207
X-RAY DIFFRACTIONr_ncsr_local_group_40.0640.0511066
X-RAY DIFFRACTIONr_ncsr_local_group_50.0630.0511153
X-RAY DIFFRACTIONr_ncsr_local_group_60.0710.0511078
X-RAY DIFFRACTIONr_ncsr_local_group_70.0660.0511102
X-RAY DIFFRACTIONr_ncsr_local_group_80.0580.0511073
X-RAY DIFFRACTIONr_ncsr_local_group_90.0650.0511149
X-RAY DIFFRACTIONr_ncsr_local_group_100.0650.0511155
X-RAY DIFFRACTIONr_ncsr_local_group_110.0630.0511100
X-RAY DIFFRACTIONr_ncsr_local_group_120.0670.0511022
X-RAY DIFFRACTIONr_ncsr_local_group_130.0670.0511118
X-RAY DIFFRACTIONr_ncsr_local_group_140.0680.0511021
X-RAY DIFFRACTIONr_ncsr_local_group_150.0680.0510985
X-RAY DIFFRACTIONr_ncsr_local_group_160.0630.0510987
X-RAY DIFFRACTIONr_ncsr_local_group_170.070.0510962
X-RAY DIFFRACTIONr_ncsr_local_group_180.0740.0510947
X-RAY DIFFRACTIONr_ncsr_local_group_190.0680.0511050
X-RAY DIFFRACTIONr_ncsr_local_group_200.0570.0511142
X-RAY DIFFRACTIONr_ncsr_local_group_210.060.0511077
X-RAY DIFFRACTIONr_ncsr_local_group_220.0710.0511080
X-RAY DIFFRACTIONr_ncsr_local_group_230.0640.0511015
X-RAY DIFFRACTIONr_ncsr_local_group_240.0740.0510990
X-RAY DIFFRACTIONr_ncsr_local_group_250.0660.0510994
X-RAY DIFFRACTIONr_ncsr_local_group_260.0680.0511073
X-RAY DIFFRACTIONr_ncsr_local_group_270.0680.0511115
X-RAY DIFFRACTIONr_ncsr_local_group_280.0760.0510943
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.06090.05009
12BX-RAY DIFFRACTIONLocal ncs0.06090.05009
23AX-RAY DIFFRACTIONLocal ncs0.067440.05009
24CX-RAY DIFFRACTIONLocal ncs0.067440.05009
35AX-RAY DIFFRACTIONLocal ncs0.057370.05009
36DX-RAY DIFFRACTIONLocal ncs0.057370.05009
47AX-RAY DIFFRACTIONLocal ncs0.064030.05009
48EX-RAY DIFFRACTIONLocal ncs0.064030.05009
59AX-RAY DIFFRACTIONLocal ncs0.063210.05009
510FX-RAY DIFFRACTIONLocal ncs0.063210.05009
611AX-RAY DIFFRACTIONLocal ncs0.071080.05009
612GX-RAY DIFFRACTIONLocal ncs0.071080.05009
713AX-RAY DIFFRACTIONLocal ncs0.065760.05009
714HX-RAY DIFFRACTIONLocal ncs0.065760.05009
815BX-RAY DIFFRACTIONLocal ncs0.058410.05009
816CX-RAY DIFFRACTIONLocal ncs0.058410.05009
917BX-RAY DIFFRACTIONLocal ncs0.064760.05009
918DX-RAY DIFFRACTIONLocal ncs0.064760.05009
1019BX-RAY DIFFRACTIONLocal ncs0.06530.05009
1020EX-RAY DIFFRACTIONLocal ncs0.06530.05009
1121BX-RAY DIFFRACTIONLocal ncs0.062920.05009
1122FX-RAY DIFFRACTIONLocal ncs0.062920.05009
1223BX-RAY DIFFRACTIONLocal ncs0.06680.05009
1224GX-RAY DIFFRACTIONLocal ncs0.06680.05009
1325BX-RAY DIFFRACTIONLocal ncs0.066980.05009
1326HX-RAY DIFFRACTIONLocal ncs0.066980.05009
1427CX-RAY DIFFRACTIONLocal ncs0.06840.05009
1428DX-RAY DIFFRACTIONLocal ncs0.06840.05009
1529CX-RAY DIFFRACTIONLocal ncs0.068350.05009
1530EX-RAY DIFFRACTIONLocal ncs0.068350.05009
1631CX-RAY DIFFRACTIONLocal ncs0.063110.05009
1632FX-RAY DIFFRACTIONLocal ncs0.063110.05009
1733CX-RAY DIFFRACTIONLocal ncs0.070040.05009
1734GX-RAY DIFFRACTIONLocal ncs0.070040.05009
1835CX-RAY DIFFRACTIONLocal ncs0.073630.05009
1836HX-RAY DIFFRACTIONLocal ncs0.073630.05009
1937DX-RAY DIFFRACTIONLocal ncs0.067740.05009
1938EX-RAY DIFFRACTIONLocal ncs0.067740.05009
2039DX-RAY DIFFRACTIONLocal ncs0.056840.05009
2040FX-RAY DIFFRACTIONLocal ncs0.056840.05009
2141DX-RAY DIFFRACTIONLocal ncs0.059980.05009
2142GX-RAY DIFFRACTIONLocal ncs0.059980.05009
2243DX-RAY DIFFRACTIONLocal ncs0.070780.05009
2244HX-RAY DIFFRACTIONLocal ncs0.070780.05009
2345EX-RAY DIFFRACTIONLocal ncs0.064360.05009
2346FX-RAY DIFFRACTIONLocal ncs0.064360.05009
2447EX-RAY DIFFRACTIONLocal ncs0.074010.05009
2448GX-RAY DIFFRACTIONLocal ncs0.074010.05009
2549EX-RAY DIFFRACTIONLocal ncs0.066450.05009
2550HX-RAY DIFFRACTIONLocal ncs0.066450.05009
2651FX-RAY DIFFRACTIONLocal ncs0.068260.05009
2652GX-RAY DIFFRACTIONLocal ncs0.068260.05009
2753FX-RAY DIFFRACTIONLocal ncs0.068170.05009
2754HX-RAY DIFFRACTIONLocal ncs0.068170.05009
2855GX-RAY DIFFRACTIONLocal ncs0.076410.05009
2856HX-RAY DIFFRACTIONLocal ncs0.076410.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.60.341970.3074114X-RAY DIFFRACTION59.6843
2.6-2.6470.1991030.1621858X-RAY DIFFRACTION98.8906
2.647-2.680.275490.251830X-RAY DIFFRACTION79.4756
2.68-2.7190.3233030.2965426X-RAY DIFFRACTION81.6562
2.719-2.7980.3273330.2846001X-RAY DIFFRACTION93.106
2.798-2.8840.3393030.2716192X-RAY DIFFRACTION98.0821
2.884-2.9780.3113230.2655958X-RAY DIFFRACTION98.3096
2.978-3.0830.3093070.2545804X-RAY DIFFRACTION98.3741
3.083-3.1990.2893270.2375585X-RAY DIFFRACTION98.5169
3.199-3.330.2762560.2315435X-RAY DIFFRACTION98.6309
3.33-3.4780.2762980.2225129X-RAY DIFFRACTION98.3865
3.478-3.6470.2612830.2284958X-RAY DIFFRACTION98.7564
3.647-3.8440.2842390.2254697X-RAY DIFFRACTION98.6608
3.844-4.0770.2182040.2134536X-RAY DIFFRACTION98.6267
4.077-4.3580.1912160.1634181X-RAY DIFFRACTION99.0985
4.358-4.7060.1742390.1413847X-RAY DIFFRACTION98.7434
4.706-5.1540.1822230.1473595X-RAY DIFFRACTION99.3495
5.154-5.7610.2171620.1723272X-RAY DIFFRACTION99.1912
5.761-6.6480.2481520.1842899X-RAY DIFFRACTION99.3487
6.648-8.1340.1951270.1722434X-RAY DIFFRACTION99.3791

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