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- PDB-4d11: GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and mang... -

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Basic information

Entry
Database: PDB / ID: 4d11
TitleGalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 peptide and manganese (Lower resolution dataset)
Components
  • (POLYPEPTIDE GALNAC-TRANSFERASE ...) x 2
  • PEPTIDE
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / RETAINING GALNAC-T2 / SUBSTRATE-GUIDED SNI-TYPE REACTION / QM/MM METADYNAMICS / BI-BI KINETIC MECHANISM / SUBSTRATE SPECIFICITY / ACETAMIDO GROUP
Function / homology
Function and homology information


intussusceptive angiogenesis / apoptotic process involved in heart morphogenesis / chorio-allantoic fusion / : / : / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / positive regulation of ceramide biosynthetic process / chondroblast differentiation ...intussusceptive angiogenesis / apoptotic process involved in heart morphogenesis / chorio-allantoic fusion / : / : / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / positive regulation of ceramide biosynthetic process / chondroblast differentiation / atrial septum morphogenesis / positive regulation of cartilage development / O-linked glycosylation of mucins / protein O-linked glycosylation / Golgi stack / extracellular matrix binding / COPI-independent Golgi-to-ER retrograde traffic / atrioventricular valve morphogenesis / positive regulation of cell-substrate adhesion / labyrinthine layer blood vessel development / ventricular septum development / Golgi cisterna membrane / positive regulation of immunoglobulin production / growth factor binding / extracellular matrix organization / reactive oxygen species metabolic process / protein maturation / positive regulation of cell differentiation / integrin binding / osteoblast differentiation / manganese ion binding / carbohydrate binding / positive regulation of cell migration / positive regulation of apoptotic process / Golgi membrane / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular region / membrane
Similarity search - Function
IGFBP-related, CNN / : / CCN, TSP1 domain / CCN3 Nov like TSP1 domain / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / N-acetylgalactosaminyltransferase / Insulin-like growth factor binding protein / Glycoprotein hormone subunit beta / Cystine-knot domain ...IGFBP-related, CNN / : / CCN, TSP1 domain / CCN3 Nov like TSP1 domain / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / N-acetylgalactosaminyltransferase / Insulin-like growth factor binding protein / Glycoprotein hormone subunit beta / Cystine-knot domain / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / von Willebrand factor type C domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Ricin-type beta-trefoil lectin domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Nucleotide-diphospho-sugar transferases / Growth factor receptor cysteine-rich domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-BBK / : / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 2 / CCN family member 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. ...Lira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. / Rovira, C. / Hurtado-Guerrero, R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2.
Authors: Lira-Navarrete, E. / Iglesias-Fernandez, J. / Zandberg, W.F. / Companon, I. / Kong, Y. / Corzana, F. / Pinto, B.M. / Clausen, H. / Peregrina, J.M. / Vocadlo, D. / Rovira, C. / Hurtado-Guerrero, R.
History
DepositionMay 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYPEPTIDE GALNAC-TRANSFERASE T2
B: POLYPEPTIDE GALNAC-TRANSFERASE T2
C: POLYPEPTIDE GALNAC-TRANSFERASE T2
D: POLYPEPTIDE GALNAC-TRANSFERASE T2
E: POLYPEPTIDE GALNAC-TRANSFERASE T2
F: POLYPEPTIDE GALNAC-TRANSFERASE T2
L: PEPTIDE
O: PEPTIDE
P: PEPTIDE
X: PEPTIDE
Z: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,42527
Polymers391,72111
Non-polymers3,70416
Water00
1
A: POLYPEPTIDE GALNAC-TRANSFERASE T2
B: POLYPEPTIDE GALNAC-TRANSFERASE T2
P: PEPTIDE
Z: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,13910
Polymers130,7474
Non-polymers1,3936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-37.5 kcal/mol
Surface area38760 Å2
MethodPISA
2
D: POLYPEPTIDE GALNAC-TRANSFERASE T2
E: POLYPEPTIDE GALNAC-TRANSFERASE T2
O: PEPTIDE
X: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,13910
Polymers130,7474
Non-polymers1,3936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-38.1 kcal/mol
Surface area38650 Å2
MethodPISA
3
C: POLYPEPTIDE GALNAC-TRANSFERASE T2
L: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8624
Polymers65,4032
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-15.4 kcal/mol
Surface area19950 Å2
MethodPISA
4
F: POLYPEPTIDE GALNAC-TRANSFERASE T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2843
Polymers64,8251
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.771, 120.898, 249.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A75 - 569
2010B75 - 569
1020A74 - 542
2020C74 - 569
1030A75 - 569
2030D75 - 569
1040A75 - 569
2040E75 - 569
1050A76 - 388
2050F76 - 562
1060B75 - 541
2060C75 - 568
1070B75 - 569
2070D75 - 569
1080B75 - 569
2080E75 - 569
1090B76 - 389
2090F76 - 562
10100C75 - 568
20100D75 - 539
10110C75 - 568
20110E75 - 539
10120C76 - 389
20120F76 - 562
10130D75 - 569
20130E75 - 569
10140D76 - 389
20140F76 - 562
10150E76 - 389
20150F76 - 562

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper: (Code: given
Matrix: (-0.08242, -0.02447, 0.9963), (0.008671, 0.9996, 0.02527), (-0.9966, 0.01072, -0.08218)
Vector: 191.041, -18.1798, 120.665)

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Components

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POLYPEPTIDE GALNAC-TRANSFERASE ... , 2 types, 6 molecules ABDEFC

#1: Protein
POLYPEPTIDE GALNAC-TRANSFERASE T2


Mass: 64824.703 Da / Num. of mol.: 5 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD-1168 / References: UniProt: Q10471
#2: Protein POLYPEPTIDE GALNAC-TRANSFERASE T2


Mass: 64854.727 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD-1168 / References: UniProt: Q10471

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Protein/peptide / Sugars , 2 types, 9 molecules LOPXZ

#3: Protein/peptide
PEPTIDE


Mass: 548.610 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD-1168 / References: UniProt: Q6FI18*PLUS
#5: Sugar
ChemComp-BBK / 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose / 2-(acetylamino)-2-deoxy-5-thio-alpha-D-galactopyranose / 2-acetamido-2-deoxy-5-thio-alpha-D-galactose / 2-acetamido-2-deoxy-5-thio-D-galactose / 2-acetamido-2-deoxy-5-thio-galactose


Type: D-saccharide, alpha linking / Mass: 237.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO5S

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Non-polymers , 2 types, 12 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 % / Description: NONE

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.96
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.85→47 Å / Num. obs: 83233 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.5
Reflection shellResolution: 2.85→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FFV

2ffv


Resolution: 2.85→249.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / SU B: 33.179 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23497 2285 2.7 %RANDOM
Rwork0.21602 ---
obs0.21655 80867 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.266 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å20 Å2
2--0.73 Å20 Å2
3----4.51 Å2
Refinement stepCycle: LAST / Resolution: 2.85→249.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21608 0 216 0 21824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01922393
X-RAY DIFFRACTIONr_bond_other_d0.0080.0221064
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.95530324
X-RAY DIFFRACTIONr_angle_other_deg2.715348304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52952680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26223.3391111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.693153811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.06715213
X-RAY DIFFRACTIONr_chiral_restr0.1050.23223
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02125274
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9394.4210797
X-RAY DIFFRACTIONr_mcbond_other3.9394.4210798
X-RAY DIFFRACTIONr_mcangle_it6.476.60513452
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2645.03611595
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A303690.08
12B303690.08
21A266130.11
22C266130.11
31A306600.09
32D306600.09
41A307440.07
42E307440.07
51A174980.11
52F174980.11
61B267080.12
62C267080.12
71B300380.09
72D300380.09
81B301820.08
82E301820.08
91B174370.11
92F174370.11
101C263560.12
102D263560.12
111C264450.11
112E264450.11
121C175620.11
122F175620.11
131D305690.09
132E305690.09
141D174760.12
142F174760.12
151E176750.11
152F176750.11
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 167 -
Rwork0.342 5887 -
obs--99.92 %
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)
10.0537-0.1776-0.05660.67680.24760.30440.0282-0.00440.0257-0.0578-0.03090.06980.004-0.03740.00270.21610.0071-0.05070.3452-0.02920.3964126.984539.349437.8487
20.29690.16140.44450.29150.25880.9184-0.038-0.13030.0458-0.21950.0484-0.0269-0.02150.0176-0.01040.3697-0.0517-0.01930.349-0.00920.2358138.603832.4406-0.778
30.45340.00520.26120.5128-0.67641.5098-0.24830.0250.1515-0.04940.1713-0.17180.0847-0.29870.0770.27760.0765-0.09470.30690.06150.2969103.062493.165621.475
40.725-0.3054-0.33130.18080.20390.34380.1095-0.07880.1831-0.08570.0534-0.09870.035-0.0363-0.16280.2948-0.04980.06730.2605-0.02370.4099125.767750.8175-43.1242
50.0991-0.20860.02880.8281-0.17470.05460.0523-0.06960.0329-0.14830.0039-0.07920.0123-0.004-0.05620.2198-0.01130.03050.28550.02450.462588.402958.2118-55.5331
60.90841.1356-0.30841.432-0.44860.4261-0.1936-0.1422-0.2982-0.1996-0.1059-0.4114-0.1601-0.30940.29950.35880.1681-0.12130.5036-0.13780.232111.067108.6374-25.5063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A74 - 600
2X-RAY DIFFRACTION2B75 - 600
3X-RAY DIFFRACTION3C74 - 600
4X-RAY DIFFRACTION4D75 - 600
5X-RAY DIFFRACTION5E75 - 600
6X-RAY DIFFRACTION6F76 - 600

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