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- PDB-6vlc: Crystal structure of UDP-GlcNAc 2-epimerase from Neisseria mening... -

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Basic information

Entry
Database: PDB / ID: 6vlc
TitleCrystal structure of UDP-GlcNAc 2-epimerase from Neisseria meningitidis bound to UDP-GlcNAc
ComponentsUDP-N-acetylglucosamine 2-epimerase
KeywordsISOMERASE / Epimerase UDP-GlcNAc UDP-ManNAc UDP-GlcNAc 2-epimerase
Function / homologyUDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / capsule polysaccharide biosynthetic process / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 2-epimerase
Function and homology information
Biological speciesNeisseria meningitidis Z2491 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFisher, A.J. / Hurlburt, N.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094523 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of a nonhydrolyzing UDP-GlcNAc 2-epimerase from Neisseria meningitidis serogroup A.
Authors: Hurlburt, N.K. / Guan, J. / Ong, H. / Yu, H. / Chen, X. / Fisher, A.J.
History
DepositionJan 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 18, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 2.1Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine 2-epimerase
B: UDP-N-acetylglucosamine 2-epimerase
C: UDP-N-acetylglucosamine 2-epimerase
D: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,6116
Polymers171,3964
Non-polymers1,2152
Water13,655758
1
A: UDP-N-acetylglucosamine 2-epimerase
B: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3063
Polymers85,6982
Non-polymers6071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-25 kcal/mol
Surface area30060 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine 2-epimerase
D: UDP-N-acetylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3063
Polymers85,6982
Non-polymers6071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-26 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.880, 129.740, 213.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain 'A' and (resid 1 through 212 or resid 219 through 371))AA1 - 2111 - 211
12GLUGLULYSLYS(chain 'A' and (resid 1 through 212 or resid 219 through 371))AA219 - 370219 - 370
21METMETALAALA(chain 'B' and (resid 1 through 212 or resid 219 through 371))BB1 - 2111 - 211
22GLUGLULYSLYS(chain 'B' and (resid 1 through 212 or resid 219 through 371))BB219 - 370219 - 370
31METMETALAALA(chain 'C' and (resid 1 through 212 or resid 219 through 371))CC1 - 2111 - 211
32GLUGLULYSLYS(chain 'C' and (resid 1 through 212 or resid 219 through 371))CC219 - 370219 - 370
41METMETALAALAchain 'D'DD1 - 2111 - 211
42GLUGLULYSLYSchain 'D'DD219 - 370219 - 370

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Components

#1: Protein
UDP-N-acetylglucosamine 2-epimerase / UDP-GlcNAc 2-epimerase


Mass: 42849.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis Z2491 (bacteria)
Strain: Z2491 / Gene: sacA, NMA0199 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0U1RGY0, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / 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: 2.55 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22% PEG-5000, 100 mM Sodium citrate/citric acid, pH 5.5, and 10 mM UDP-GlcNAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03317 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.15→38.97 Å / Num. obs: 92958 / % possible obs: 98.8 % / Redundancy: 3.753 % / Biso Wilson estimate: 33.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Χ2: 0.979 / Net I/σ(I): 18.68 / Num. measured all: 348834 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.213.590.482.4524367688667870.7360.56498.6
2.21-2.273.7570.3963.1225095669166790.8170.46399.8
2.27-2.333.7580.3173.924499653065190.8720.37199.8
2.33-2.43.7680.2754.5223997638763680.8990.32299.7
2.4-2.483.7680.2215.6223062613761210.9280.25899.7
2.48-2.573.7680.1826.8722575600959920.9530.21299.7
2.57-2.673.7670.1498.4321491572857050.9670.17499.6
2.67-2.783.770.11810.4920836555755270.980.13899.5
2.78-2.93.7760.09413.1420070534653150.9870.1199.4
2.9-3.043.7770.07616.0219081509050520.9910.08899.3
3.04-3.213.7870.05521.4618255487048200.9960.06399
3.21-3.43.7680.04426.4917101458345390.9970.05199
3.4-3.633.7780.03334.1216135433542710.9980.03898.5
3.63-3.933.7720.02840.1115081406439980.9990.03298.4
3.93-4.33.7630.02445.9313789373436640.9990.02898.1
4.3-4.813.7440.02151.9512261337532750.9990.02597
4.81-5.553.7290.02349.710720299528750.9990.02696
5.55-6.83.7040.02447.279145257424690.9990.02795.9
6.8-9.623.8330.01758.817336201319140.9990.0295.1
9.62-38.973.6870.01467.183938117610680.9990.01690.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSJanuary 10, 2014data reduction
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F6D

1f6d


Resolution: 2.15→38.97 Å / SU ML: 0.2453 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2675
RfactorNum. reflection% reflection
Rfree0.2117 2006 2.16 %
Rwork0.1679 90935 -
obs0.1689 92941 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11602 0 78 758 12438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211912
X-RAY DIFFRACTIONf_angle_d1.492116205
X-RAY DIFFRACTIONf_chiral_restr0.08621948
X-RAY DIFFRACTIONf_plane_restr0.00962041
X-RAY DIFFRACTIONf_dihedral_angle_d10.60277325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.31071380.25066410X-RAY DIFFRACTION98.56
2.2-2.260.29081400.22666469X-RAY DIFFRACTION99.79
2.26-2.330.26781530.21656504X-RAY DIFFRACTION99.85
2.33-2.410.30341320.21026514X-RAY DIFFRACTION99.67
2.41-2.490.2511490.19966537X-RAY DIFFRACTION99.73
2.49-2.590.22571350.19246455X-RAY DIFFRACTION99.68
2.59-2.710.23241560.18446522X-RAY DIFFRACTION99.58
2.71-2.850.28061360.18126501X-RAY DIFFRACTION99.52
2.85-3.030.21551440.18646500X-RAY DIFFRACTION99.3
3.03-3.260.24021440.17246504X-RAY DIFFRACTION99
3.26-3.590.22121460.16286525X-RAY DIFFRACTION98.93
3.59-4.110.17931480.14446490X-RAY DIFFRACTION98.28
4.11-5.180.15441410.12536465X-RAY DIFFRACTION97.19
5.18-38.970.16841440.15436539X-RAY DIFFRACTION95.28
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)
12.096595329550.304920949624-0.945803248122.929697543942.304035316572.59017420830.007494597068590.03582041929210.137939223214-0.4570090659140.0175278802319-0.0775778906236-0.3886721339750.112683711478-0.005120376435510.2992201079770.001549413452010.02649799549550.2847691054060.1110276222840.2419105419949.086453153691.0937859306-13.7074560356
22.39696622039-1.200372588240.3471000169872.18453043804-0.4950978980640.80460983083-0.104075227849-0.252580735778-0.2044093069310.1597143708630.1433589480530.32093542663-0.109553053194-0.154785748166-0.01048651278920.2374726465670.01984675325290.03718148936170.2965933674490.08613619027810.202723170705-12.034763515793.0039985654-5.59851254514
30.3276368261010.5035711512220.5277244572582.203096042570.7596084073731.10718141698-0.01800185128440.111607376149-0.0588387698868-0.07909771914640.1070645398350.0149200914541-0.07805049744820.0296187492737-0.08209159485070.196669916207-0.01677436668730.01350146549750.2860309229210.05113591767170.3526323349580.53578869118364.3673485871-29.4538748614
45.80542185537-1.526650766362.956322003572.49280861484-2.498735094978.651485507320.2097074378220.63070203933-0.536374016524-0.468787182746-0.26736149268-0.1050502018320.382588028590.2932408412280.1263891749040.308115360110.09673651532490.05098076928280.34403860329-0.03708344520480.31666009478917.12468893234.9272659575-31.6255049739
53.15184592531-0.825452015440.9551760919671.66271668358-1.026206058371.627245698370.08679269540290.0296052497473-0.166311747881-0.0567791763844-0.111849483644-0.07904241732990.2184099805190.225868211344-0.01195414972610.225026969536-0.0545532095781-0.003151722592160.2600656081330.006585806981210.18837034312410.79453496339.4366422331-23.9695227951
63.44618908597-0.0228128961061.522872228982.46311821548-1.466724539971.89136125528-0.0555503055931-0.644998578654-0.087943739521-0.0634776580530.3280996913250.5286636281590.196390849453-0.551886426253-0.1729830673940.275227563599-0.03772780386840.02730232281720.3532178990920.09824067732880.300256779214-28.7473950654119.365104635-39.4406404233
72.09520878157-1.13985736450.741818128352.83003280588-0.5571361686132.46262030056-0.018539368912-0.01775768707740.177484858537-0.3009541364780.0207768415214-0.3703093807780.07178230687620.01944201022030.02828717030.209891501672-0.01430994695770.06612814832550.139257963516-0.01091374171910.189349701333-16.5840957734126.513093253-46.0996345168
85.707974725292.001207793570.05114404816381.509297414161.145271949521.950890773780.3098232178951.003049154020.240663139432-1.11432669070.02448542768291.26432278415-0.14303177132-1.06183155211-0.3153646657580.5448984798960.0265475745581-0.2144559066110.9089103794050.1750481759920.702187503652-48.64000258141.503967268-52.6439835829
91.49340142218-1.41768379929-0.6870305034033.599334727321.128678549620.9759307586750.2160705779790.06257813285290.329767091408-0.431124454442-0.0251692789847-0.160840633674-0.179748790727-0.0971018634344-0.1772082149030.3101273208320.007374867598110.03293511261940.2067595058090.04930934939630.221626907823-30.0769885924145.655633249-47.0618467743
103.30897516977-0.0172808581370.4374887363970.358560916678-0.1761015054530.588626626619-0.128367286768-0.668668164710.4726438729350.1797164405020.128007503912-0.172552809863-0.0910183357451-0.0393013020034-0.02589687688970.2907419763830.0747711366209-0.03153862036740.331337498694-0.1519103654610.3787867733680.748675184094126.781424772-23.8846720315
112.9543760888-1.45238131803-2.27931898185.450910516933.595619259068.61772089075-0.206286003792-0.588640894035-0.1698872058620.8983502909260.017819542577-0.4480301207470.368470015510.1613178773460.08961228402410.3692954857820.0295609559377-0.08882691394760.2862844935020.05305398040810.28804761713229.6053349304109.157769399-21.6946885506
122.34981973862-0.19502887624-0.1769594904773.260102276670.8162914663441.85745462279-0.163436206156-0.163385892620.04097356752940.0160677543018-0.005885077313010.04291591915540.134238437703-0.004739039806780.1358515843090.231842410186-0.0240292946373-0.04341001090180.195095037452-0.006204158765970.18434273213325.386462492115.657222271-29.5564563886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:108)
2X-RAY DIFFRACTION2(chain A and resid 109:371)
3X-RAY DIFFRACTION3(chain B and resid 1:185)
4X-RAY DIFFRACTION4(chain B and resid 186:234)
5X-RAY DIFFRACTION5(chain B and resid 235:371)
6X-RAY DIFFRACTION6(chain C and resid 1:85)
7X-RAY DIFFRACTION7(chain C and resid 86:185)
8X-RAY DIFFRACTION8(chain C and resid 186:205)
9X-RAY DIFFRACTION9(chain C and resid 206:371)
10X-RAY DIFFRACTION10(chain D and resid 1:185)
11X-RAY DIFFRACTION11(chain D and resid 186:234)
12X-RAY DIFFRACTION12(chain D and resid 235:371)

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