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- PDB-7pe4: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -

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Basic information

Entry
Database: PDB / ID: 7pe4
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP-glucose
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP-glucose / thermostable / GTA-fold
Function / homologyglucosyl-3-phosphoglycerate synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / BICARBONATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glucosyl-3-phosphoglycerate synthase
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSilva, A. / 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 UDP-glucose
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 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)36,0319
Polymers35,1511
Non-polymers8808
Water5,495305
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,06218
Polymers70,3022
Non-polymers1,76016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area8850 Å2
ΔGint-122 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.887, 101.887, 122.098
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
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucosyl-3-phosphoglycerate synthase /


Mass: 35151.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal 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 (E. coli)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 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: 0.96112 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013 / Details: 0.96112
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 38917 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.73 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 14.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3768 / Rrim(I) all: 1.052 / % possible all: 99.6

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Processing

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

7p8g


Resolution: 2.05→46.58 Å / SU ML: 0.2325 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192 1950 5.02 %
Rwork0.1602 36928 -
obs0.1618 38878 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 52 306 2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642477
X-RAY DIFFRACTIONf_angle_d0.80843395
X-RAY DIFFRACTIONf_chiral_restr0.0512409
X-RAY DIFFRACTIONf_plane_restr0.0107440
X-RAY DIFFRACTIONf_dihedral_angle_d12.3845926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.3031460.27732595X-RAY DIFFRACTION99.38
2.1-2.160.2871290.25022593X-RAY DIFFRACTION99.45
2.16-2.220.26141290.22742630X-RAY DIFFRACTION99.78
2.22-2.290.23391440.20322632X-RAY DIFFRACTION99.61
2.29-2.380.24791390.1952648X-RAY DIFFRACTION99.93
2.38-2.470.27721340.18852637X-RAY DIFFRACTION99.89
2.47-2.580.21581620.18742594X-RAY DIFFRACTION99.71
2.58-2.720.221350.18042648X-RAY DIFFRACTION99.89
2.72-2.890.23081360.17972646X-RAY DIFFRACTION99.86
2.89-3.110.20321410.17722646X-RAY DIFFRACTION99.96
3.11-3.430.1861410.1472639X-RAY DIFFRACTION99.93
3.43-3.920.13771470.12172673X-RAY DIFFRACTION99.96
3.92-4.940.14561250.11532668X-RAY DIFFRACTION99.96
4.94-46.580.1731420.15822679X-RAY DIFFRACTION99.75
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)
10.921259226957-0.2233255178830.3343627299552.0828481258-0.4932910631482.217271119920.0886143656823-0.0691307499996-0.195772091879-0.1403060808360.0704226611130.2739815093210.33992580703-0.330610790703-0.1221369281660.334072230266-0.126038668581-0.01096741065680.306782493890.05967861796920.3033845045981.45426991151-25.1545693764.25259797548
25.20638638297-0.082613812203-2.497831965221.75701657026-0.05496568170685.464298147710.071368486418-0.0917896371988-0.02326914569630.00722450405939-0.0175488402581-0.1207779477880.1880587596940.123488741203-0.06277344419180.305139721282-0.00108940490018-0.02586175446310.1733423107310.05759761188140.2565554951513.4713153831-24.09578689670.414034501744
36.081036178731.216619708840.5227518197368.890621381530.8691872531066.123387794390.09313701089220.0477858077218-0.294512427226-0.3170084091230.2038956340620.7656826110970.143073449202-0.673935827686-0.1899345894270.301391819629-0.122508039829-0.03885645549760.3475091959580.1278848486110.363237275369-5.00377798185-26.34410471731.65713295671
44.13341950511-0.177951634443-0.09982086164336.124196520921.577987746620.5544341585650.0111843288752-0.99684162054-0.3504442690180.738388255955-0.0983598440210.2312685271810.590950447749-0.366382415510.09037809632310.349958845197-0.004467926079820.07284515155550.4961665600930.08774901933450.386056388315-4.26736491756-6.095943318532.22563611285
52.97720581572-1.95901559790.8525859578063.14382696287-0.1804714041232.847530245950.128538635942-0.110133661975-0.0667969312446-0.15781853401-0.05082981250520.1826132660990.28479565991-0.214277233037-0.0765270479610.30282123253-0.0678535385050.006595424236320.3336359616810.04975516016890.3186600444970.911233755755-17.526864672-6.38223103895
63.983954577372.35671709658-2.170231634575.46677680289-2.074265090491.343262031690.286740511727-0.6706125710570.2722863289370.911366000306-0.4829921083440.174822707548-0.2550186774110.3798527126890.2354746121630.375538629143-0.0861514421268-0.04019623880070.4879893337690.100493059440.373143688515-2.42019331056-15.63953179336.95883024197
75.962271122861.187518571650.4117106918096.01347332202-1.036525455665.26065651466-0.0254715063881-0.569637000460.09489172434770.1059633449-0.0559047279899-0.335039397364-0.200441600128-0.04077707285620.0756038636040.1913346966060.04814676606110.02588894140960.3282414075950.00500143997690.3355324003218.20495778612-1.06515299052-3.40274076974
83.198624129320.09876158044990.2092282136593.489892389562.286498191555.983298430750.0725929692824-0.3577418297850.1238301976570.0383704691288-0.0470449429203-0.5500763984750.0968648238490.0624917625224-0.07950320648140.1897535078660.016297214540.03790381052790.3795514316160.02906969759380.2924007060616.0112252124-11.573156463-7.09476063275
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 93 )2 - 931 - 92
22chain 'A' and (resid 94 through 140 )94 - 14093 - 139
33chain 'A' and (resid 141 through 163 )141 - 163140 - 162
44chain 'A' and (resid 164 through 192 )164 - 192163 - 181
55chain 'A' and (resid 193 through 237 )193 - 237182 - 226
66chain 'A' and (resid 238 through 256 )238 - 256227 - 245
77chain 'A' and (resid 257 through 289 )257 - 289246 - 278
88chain 'A' and (resid 290 through 321 )290 - 321279 - 310

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