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- PDB-7pd5: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7pd5
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with 4-aminobenzoic acid
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP / thermostable / GTA-fold
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
4-AMINOBENZOIC ACID / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSilva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221). Portugal
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with 4-aminobenzoic acid
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Feb 7, 2024Group: 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: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6758
Polymers35,1511
Non-polymers5247
Water1,49583
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,35016
Polymers70,3022
Non-polymers1,04714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area7290 Å2
ΔGint-121 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.272, 100.272, 123.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Glucosyl-3-phosphoglycerate synthase


Mass: 35151.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence KLAAALEHHHHHH corresponds to the linker and hexahistidine tag used for protein purification
Source: (gene. exp.) Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-PAB / 4-AMINOBENZOIC ACID


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5 3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.95→46.65 Å / Num. obs: 44461 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 52.01 Å2 / CC1/2: 1 / Net I/σ(I): 15.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 14143 / CC1/2: 0.419 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8G

7p8g


Resolution: 1.95→46.65 Å / SU ML: 0.2733 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 2177 4.91 %
Rwork0.1866 42117 -
obs0.1877 44294 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 29 83 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672289
X-RAY DIFFRACTIONf_angle_d0.88583132
X-RAY DIFFRACTIONf_chiral_restr0.0556385
X-RAY DIFFRACTIONf_plane_restr0.0096402
X-RAY DIFFRACTIONf_dihedral_angle_d12.749825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.43121240.42592587X-RAY DIFFRACTION97.41
1.99-2.040.38541680.37692570X-RAY DIFFRACTION99.24
2.04-2.090.37281400.34052648X-RAY DIFFRACTION99.57
2.09-2.150.29961420.31072588X-RAY DIFFRACTION99.56
2.15-2.210.31111390.29042639X-RAY DIFFRACTION99.5
2.21-2.280.26941250.26682627X-RAY DIFFRACTION99.57
2.28-2.360.29751390.25872632X-RAY DIFFRACTION99.78
2.36-2.460.22021310.22732641X-RAY DIFFRACTION99.93
2.46-2.570.25061330.23112643X-RAY DIFFRACTION99.75
2.57-2.70.2511490.21672627X-RAY DIFFRACTION99.93
2.7-2.870.28731380.24762648X-RAY DIFFRACTION100
2.87-3.10.26731070.21982659X-RAY DIFFRACTION99.82
3.1-3.410.20831430.20782630X-RAY DIFFRACTION99.86
3.41-3.90.19861470.15892635X-RAY DIFFRACTION99.68
3.9-4.910.14571290.13312647X-RAY DIFFRACTION99.28
4.91-46.650.16931230.15212696X-RAY DIFFRACTION99.44
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)
12.40762507752-1.682611623062.141839843575.475079228030.1092414049522.86003430429-0.142719909016-0.1950963159550.0289194282249-0.4738811408260.3420617149570.6212987274680.160227086053-1.1691438789-0.2122884549410.641037732142-0.2042440728630.04221168686311.000232151010.2688978038230.884755647218-12.5334545094-21.80721755411.05674000324
23.436282542160.670529421666-0.1570201487722.7677023791-0.5859630277265.362731929220.0247636224672-0.308297960543-0.2887011521860.1736908532040.0277086694273-0.07678322631450.4769892275610.240568153319-0.0528675166760.5412843462630.002415345911380.001488632514860.4051471001610.0752954412740.46512070240913.0234801923-27.750701342111.1439546254
34.90828170902-1.08675221774-1.297041389531.003719353040.36423588915.733308050320.150689559013-0.03580038693320.0440480395763-0.213106313445-0.0905470796829-0.262028205870.2572047698060.386273642188-0.05100948535250.611619208371-0.008148361955850.009775390837090.4463336402410.06226186627090.54094207358718.9608876411-22.5123808396-1.36885321058
44.53975022406-0.3245329365930.4746475573024.37980651255-1.125486369125.161910949680.0361736996497-0.1943507030330.04610074611330.2777929927140.1585095946810.7525144766660.286264171812-0.864580463165-0.1811532847490.556373810028-0.08416418792050.03995183057420.6148327557180.1443599407170.592295529356-0.0904994750918-25.19739976786.48806907841
52.99650508783-2.14778487072-0.1580733485774.72766360834-1.734126937342.3725947609-0.113065078001-0.679849732857-0.5094275215920.4327058086140.4214231568750.4031680345370.0889586372247-0.62252219928-0.2902810002070.4398480336540.02498895518040.05011118661990.6472478444590.1241315360580.48856355199-4.45810457493-8.999532439680.88685925062
63.41024883485-0.185709058149-0.3442195340222.52923793115-1.083038437681.522054768930.247524357837-0.07786842583420.0386128753515-0.191066038088-0.1367793645130.1738105745740.348115798724-0.174861718079-0.09637965088390.541144743584-0.0464327629262-0.01013993950680.5926128104020.06093726836330.5037706967763.70449580195-19.2736886066-5.88717408716
72.110607042350.498343941891-1.177492307835.14313842053-1.425087681822.97150215969-0.1536497162350.04694028815980.1688881697610.8102261628350.2117831612580.545803364226-0.772778614050.752318734432-0.09069524557510.610515557445-0.07421321634140.03340089824830.9161953509610.2317117756320.601954357897-3.49638094208-16.78973187097.45125117527
86.34612673655-0.568959823946-1.076712230696.241359812270.9196684360574.78969669941-0.126404844557-0.6504260548370.376845475430.2337485645480.201649394253-0.66827885197-0.09700370476640.672738511655-0.06889565090580.5078468162160.07568386387810.0153791574320.681708131127-0.02747654733740.5943273897139.266686873910.0818480817682-0.517534243503
97.17649723207-0.507844528133-0.4926345487133.082005442951.535852164978.137207241570.09318480018020.076351011666-0.527617791032-0.347355291273-0.000692044478992-0.1657386997660.6923751076290.110866140228-0.1244603157240.6036604443490.02939743110470.05875669830090.5870782022170.06387719764780.48447309236615.5232357707-20.1552630214-10.1726518256
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 37 )2 - 371 - 36
22chain 'A' and (resid 38 through 93 )38 - 9337 - 92
33chain 'A' and (resid 94 through 121 )94 - 12193 - 120
44chain 'A' and (resid 122 through 178 )122 - 178121 - 165
55chain 'A' and (resid 179 through 206 )179 - 206166 - 193
66chain 'A' and (resid 207 through 237 )207 - 237194 - 224
77chain 'A' and (resid 238 through 256 )238 - 256225 - 243
88chain 'A' and (resid 257 through 298 )257 - 298244 - 281
99chain 'A' and (resid 299 through 320 )299 - 320282 - 303

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