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- PDB-8brz: Room-temperature structure of Pedobacter heparinus N-acetylglucos... -

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Basic information

Entry
Database: PDB / ID: 8brz
TitleRoom-temperature structure of Pedobacter heparinus N-acetylglucosamine 2-epimerase at 52 MPa helium gas pressure in a sapphire capillary
ComponentsN-acylglucosamine 2-epimerase
KeywordsISOMERASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature / sialic acid synthesis / (alpha/alpha)6 barrel
Function / homology
Function and homology information


N-acylglucosamine 2-epimerase / N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process
Similarity search - Function
N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / N-acylglucosamine 2-epimerase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLieske, J. / Saouane, S. / Assmann, M. / Zaun, H. / Kuballa, J. / Meents, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0405A Germany
CitationJournal: To Be Published
Title: High-pressure macromolecular crystallography to explore the conformational space of proteins
Authors: Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Reinke, P.Y.A. / Falke, S. / Ewert, W. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Assmann, M. / Zaun, H. / Kuballa, J. / Chapman, H.N. / Meents, A.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylglucosamine 2-epimerase
B: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9996
Polymers97,7382
Non-polymers2614
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-52 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.410, 94.080, 81.710
Angle α, β, γ (deg.)90.000, 102.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein N-acylglucosamine 2-epimerase


Mass: 48868.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (bacteria) / Gene: Phep_3251 / Production host: Escherichia coli (E. coli) / References: UniProt: C6Y403
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.6 mg/ml protein in 20 mM sodium phosphate buffer pH 7.5 were mixed (4+2 ul) with 0.1 M sodium cacodylate buffer pH 5.0, 0.35 M sodium acetate and 26% PEG 8000. Crystals grew at room temperature in 5-7 days.
Pressure: 101.325 kPa

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Data collection

DiffractionAmbient environment: gaseous He / Ambient pressure: 52000 kPa / Mean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.477 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Jun 15, 2020
Diffraction measurementSpecimen support: sapphire capillary
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.477 Å / Relative weight: 1
ReflectionResolution: 1.7→41.28 Å / Num. obs: 88642 / % possible obs: 96.35 % / Redundancy: 7.9 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.2875 / Rpim(I) all: 0.1042 / Rrim(I) all: 0.3072 / Net I/σ(I): 5.64
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6 % / Rmerge(I) obs: 1.751 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 8015 / CC1/2: 0.242 / CC star: 0.624 / Rpim(I) all: 0.6563 / Rrim(I) all: 1.892 / % possible all: 82.55
Cell measurementPressure: 52000 kPa

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.18-3855_9999refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GZ6

2gz6


Resolution: 1.7→41.28 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183 1524 1.73 %
Rwork0.1575 86548 -
obs0.1579 88072 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 12 474 6890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00396860
X-RAY DIFFRACTIONf_angle_d0.68669331
X-RAY DIFFRACTIONf_chiral_restr0.0403920
X-RAY DIFFRACTIONf_plane_restr0.00391225
X-RAY DIFFRACTIONf_dihedral_angle_d26.5443907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.35531190.29666704X-RAY DIFFRACTION82.61
1.75-1.820.26941230.25837164X-RAY DIFFRACTION87.86
1.82-1.890.26251340.23847568X-RAY DIFFRACTION92.95
1.89-1.980.26551410.21778021X-RAY DIFFRACTION98.95
1.98-2.080.22411440.18928134X-RAY DIFFRACTION99.8
2.08-2.210.17531430.15818131X-RAY DIFFRACTION100
2.21-2.380.17921440.15628141X-RAY DIFFRACTION99.78
2.38-2.620.18511440.15138170X-RAY DIFFRACTION99.83
2.62-30.21891430.14728141X-RAY DIFFRACTION99.51
3-3.780.14381440.12738196X-RAY DIFFRACTION99.68
3.78-41.280.12471450.12098178X-RAY DIFFRACTION98.86
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)
11.030571444310.371545928648-0.3794434960951.47066172375-0.2244901568842.29111994710.00788537405845-0.0843610948167-0.05377906993650.149854273362-0.00885480209438-0.1001835264770.09252761558750.1725145427520.01156355491240.07873965439920.0324582621601-0.02076608082680.1149706527330.002286898093370.12931336941915.1483442295-19.616505074510.802925661
21.50341902809-1.882987959230.2513765024837.805681595741.676851277965.4327917658-0.04956361878460.1277328087470.0341952596457-0.0876222065254-0.1127992239050.708697283918-0.398942049315-0.5355138633870.09618075933440.1471654424580.000883486298283-0.01077445154780.162711874980.02143994273360.18026148047711.4979295599-3.03142117733-2.58766564784
33.77301617293-2.72242669508-1.387313723586.93458979914-1.222433813693.097608358030.08712805961250.2073884298150.169254414562-0.202256221564-0.07571492250130.111986280345-0.14642105852-0.01745799740410.01394155446560.105371040165-0.02926030180550.002448385322550.100674968416-0.02945172299090.1288323138869.65108775762-0.4269299778913.5183452781
46.413292114371.131049908195.587485845240.3020356563231.138743363165.09005578551-0.2523517033650.2012497972830.348378086868-0.05773432970750.00422542634890.00992860830137-0.323694309560.1936552630610.266019644880.151103167513-0.02077723547510.004465673140960.12257509596-0.004727416637060.156109123995-3.36910750653-4.5453051223311.0143903471
58.553346663733.018700176573.501217067541.90714374221.880428614242.40583506613-0.0987408826799-0.1425786606190.555213786771-0.0816037003703-0.1261805780470.268055859415-0.186492882956-0.1356434513070.231491821070.1613456505130.0203528009729-0.00150141208720.116675461042-0.01804574258490.179479954689-6.14418783546-1.1175295142218.4799012917
60.794701629178-0.0272287573829-0.01371711782370.6908418788860.1323998319041.24933073307-0.0141072102718-0.0408877194635-0.04822514622280.0866462754715-0.02332951193960.06060490556320.0830298938973-0.1096509972830.03768046406420.107474152349-0.02669798645050.01907719411990.09611165635790.0009280812013530.118922426662-8.77465397597-21.00360052539.65983418065
72.92459589030.225586938695-0.4340831974422.73255342447-0.9797341499755.859490780380.0279048354317-0.2955339119880.06967697438260.384188950712-0.0006672375545040.110534973315-0.230683269686-0.0771352317083-0.02586969222340.1003397145060.00396328082313-0.009363590493540.0598862439954-0.01303157239060.1329308795715.51308668954-21.955433727416.2320153592
80.6861905601850.292079513913-0.2078954545073.048580347910.7613279635481.957455157690.01115138659030.1852069316940.0456127542394-0.2492607793950.01322667526960.1359486016-0.175533114795-0.297665483337-0.05076024157870.1083195052490.0288757770159-0.0442328618670.2385010028970.03254403362810.151633319486-18.9685819829-12.2103807399-25.3345942843
97.373006186452.023345447231.540991219114.570618967560.6899666749113.10936693603-0.05726701548160.0545554843630.46653125862-0.1170285521950.1255805899110.0270918071129-0.477917285059-0.283778645072-0.003425794686750.3162153348670.1098565359950.02100003907160.1977620143410.05251347760820.197017544987-9.59403165782-0.774689608437-33.1183999202
104.34527883849-1.96200063263.94250017971.14730451274-2.344960223244.79673624897-0.142341807770.01393783286220.2920246066730.0060210191459-0.0310473296447-0.0132297308988-0.441694137467-0.04869591461460.1337109915340.2711471051570.0183755971781-0.001416164954340.1549181093740.02717969112510.1606836134760.985345667712-8.56149067421-30.2163573096
110.87975049601-0.0865127075851-0.1968618744670.644919170816-0.1683588573021.50878431705-0.02719758268470.133483483561-0.00622989624731-0.146749185502-0.00977507835111-0.007099408293960.0944378482767-0.04147217047480.03436372269780.144949148721-0.01002760135610.002593080758770.0931439746738-0.009340812655310.0930328144373-1.54249820284-23.3810093078-27.7202012013
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 95 )AA4 - 951 - 94
22chain 'A' and (resid 96 through 120 )AA96 - 12095 - 120
33chain 'A' and (resid 121 through 158 )AA121 - 158121 - 160
44chain 'A' and (resid 159 through 192 )AA159 - 192161 - 186
55chain 'A' and (resid 193 through 212 )AA193 - 212187 - 210
66chain 'A' and (resid 213 through 366 )AA213 - 366211 - 369
77chain 'A' and (resid 367 through 397 )AA367 - 397370 - 403
88chain 'B' and (resid 4 through 120 )BB4 - 1201 - 121
99chain 'B' and (resid 121 through 158 )BB121 - 158122 - 159
1010chain 'B' and (resid 159 through 192 )BB159 - 192160 - 186
1111chain 'B' and (resid 193 through 397 )BB193 - 397187 - 396

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