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

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Basic information

Entry
Database: PDB / ID: 7pdo
TitleCrystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 5.5 in complex with UDP
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 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 UDP
Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S.
History
DepositionAug 5, 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)35,5596
Polymers35,0131
Non-polymers5465
Water3,297183
1
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,11812
Polymers70,0262
Non-polymers1,09210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area6990 Å2
ΔGint-119 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.338, 101.338, 122.532
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: 35012.984 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 DSM 44199 (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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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

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: 0.96112 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 43448 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.16 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 17.1
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4232 / Rpim(I) all: 0.371 / Rrim(I) all: 0.957 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P8G

7p8g


Resolution: 1.97→46.57 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1954 2184 5.03 %
Rwork0.1822 41200 -
obs0.1829 43384 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.77 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 29 183 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652355
X-RAY DIFFRACTIONf_angle_d0.85193221
X-RAY DIFFRACTIONf_chiral_restr0.0542389
X-RAY DIFFRACTIONf_plane_restr0.0105413
X-RAY DIFFRACTIONf_dihedral_angle_d12.2467863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.33211520.31442547X-RAY DIFFRACTION98.68
2.01-2.060.24941210.26932540X-RAY DIFFRACTION98.63
2.06-2.110.27141440.24972552X-RAY DIFFRACTION99.19
2.11-2.170.26751340.22752551X-RAY DIFFRACTION98.97
2.17-2.230.26241240.21032578X-RAY DIFFRACTION99.34
2.23-2.30.2481230.20442588X-RAY DIFFRACTION99.09
2.3-2.390.22611440.20452533X-RAY DIFFRACTION99.48
2.39-2.480.25341370.21022586X-RAY DIFFRACTION99.6
2.48-2.590.25561350.2062560X-RAY DIFFRACTION99.48
2.6-2.730.25961150.20892613X-RAY DIFFRACTION99.82
2.73-2.90.24731610.2272567X-RAY DIFFRACTION99.96
2.9-3.130.25331400.22432573X-RAY DIFFRACTION99.63
3.13-3.440.21351310.18792578X-RAY DIFFRACTION99.93
3.44-3.940.15091450.1492594X-RAY DIFFRACTION99.96
3.94-4.960.12481400.12682609X-RAY DIFFRACTION99.96
4.96-46.570.15581380.16512631X-RAY DIFFRACTION99.89
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)
11.422171216470.225516595556-0.1958387364931.73228825872-0.6600605073572.289182908220.07047551864050.09915824287450.127259680750.1579535315750.07967886183550.171553274956-0.383226066272-0.312831022152-0.1420391213620.4189462269330.122400182250.02803753653080.3285058812910.05137733134330.3247277928614.93549667103-25.6785466728-36.4262572306
20.7463680789290.869097690377-0.4661085831272.81383980691-0.9127767134131.876404979810.06520356791430.1590541047370.156920306192-0.0008204959877010.1092426634490.323412626185-0.242009364744-0.431318913619-0.1779355741450.3572347616850.09779254196430.01020348299610.4572501024280.05793245560290.3350425065180.961772960785-30.6525283235-33.023426243
33.161661832870.1381381523551.473349013265.16919145009-2.473083206961.959025851920.2195562997240.5524153108390.117288943494-0.374350679769-0.02696438292870.0008146372113310.1020188810280.0191796128429-0.1647246971650.3380450593930.07710069333530.007585750580.5627162124870.0796903010810.297790374193-0.732102281015-34.70098029-32.6606473696
44.00434451233-0.916513514646-0.7567390027496.658168798622.081246730538.09603896604-0.03281247162810.458163910432-0.204149233323-0.1908754044970.114694635239-0.3458895651450.2568740148120.392371611535-0.07028056929770.345085055546-0.0493170781192-0.02615632049540.539937540218-0.0169778271410.4348096801139.46428290064-49.8911742214-30.1879123771
52.439951196942.82777601022.815457917229.230157372715.979637498174.50812613762-0.00518148039009-0.003170445426380.3921743965350.4640157561780.0546955061399-0.513469119627-0.4041864940520.104530618234-0.01889841309210.433207773227-0.00892832832169-0.04109817001680.4090067919070.03317342331390.41153284798215.5104913216-27.6398697939-19.2940533129
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 110 )2 - 1101 - 109
22chain 'A' and (resid 111 through 221 )111 - 221110 - 209
33chain 'A' and (resid 222 through 256 )222 - 256210 - 244
44chain 'A' and (resid 257 through 301 )257 - 301245 - 282
55chain 'A' and (resid 302 through 320 )302 - 320283 - 301

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