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- PDB-6wfv: The crystal structure of a collagen galactosylhydroxylysyl glucos... -

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Basic information

Entry
Database: PDB / ID: 6wfv
TitleThe crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human
ComponentsMultifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
KeywordsTRANSFERASE / Manganese / UDP / Magnesium / Rossmann fold
Function / homology
Function and homology information


procollagen galactosyltransferase / procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen galactosyltransferase activity / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / basement membrane assembly / epidermis morphogenesis ...procollagen galactosyltransferase / procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen galactosyltransferase activity / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / L-ascorbic acid binding / collagen fibril organization / neural tube development / lung morphogenesis / small molecule binding / rough endoplasmic reticulum / trans-Golgi network / protein localization / vasodilation / collagen-containing extracellular matrix / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsGuo, H.-F. / Tsai, C.-L. / Miller, M.D. / Phillips Jr., G.N. / Tainer, J.A. / Kurie, J.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA105155 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K99CA225633 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160652 United States
CitationJournal: To Be Published
Title: The crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human
Authors: Guo, H.-F. / Tsai, C.-L. / Miller, M.D. / Phillips Jr., G.N. / Tainer, J.A. / Kurie, J.M.
History
DepositionApr 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9656
Polymers28,3351
Non-polymers6305
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.066, 71.066, 110.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3


Mass: 28335.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLOD3 / Details (production host): pET-28b derived vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami 2 (DE3)
References: UniProt: O60568, procollagen-lysine 5-dioxygenase, procollagen galactosyltransferase, procollagen glucosyltransferase

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Non-polymers , 5 types, 234 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine 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
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8556.85
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop7.50.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose
2772vapor diffusion, sitting drop7.50.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose, crystal soaked in higher Mn and UDP-Glc prior to flash cooling.
2773vapor diffusion, sitting drop7.50.2 M magnesium chloride, 30% PEG 400, 0.1 M HEPES, pH 7.5. Additive: 0.002 M manganese chloride, 0.01 M UDP-Galactose. Crystal soaked in 1 M NaI prior to flash cooling

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
31003N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.1271
SYNCHROTRONALS 8.3.121.1158
SYNCHROTRONALS 8.3.131.7136
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJun 2, 2016
DECTRIS PILATUS3 6M2PIXELOct 12, 2016
DECTRIS PILATUS3 6M3PIXELSep 15, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
3Si(111)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.12711
21.11581
31.71361
Reflection

Biso Wilson estimate: 31.679 Å2 / Entry-ID: 6WFV

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRrim(I) allΧ2Diffraction-IDNet I/σ(I)
1.7-41.183639399.717.5210.9990.1170.120.886119.67
1.96-41.22294296.416.410.0370.038255.2
2.23-61.51357883.729.610.1310.134322.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.749.9691.642.125451264925530.7171.7396.4
1.74-1.7912.411.3493.0432216260025960.8691.40799.8
1.79-1.8416.3041.0884.5741234252925290.9471.123100
1.84-1.919.3880.8686.447171243424330.9770.891100
1.9-1.9619.1110.6818.1945867240024000.9850.7100
1.96-2.0318.8210.49510.3543251229822980.990.508100
2.03-2.118.0740.4212.7840071221722170.9940.433100
2.1-2.1919.9620.35815.4542939215121510.9940.367100
2.19-2.2920.0610.28518.2741726208020800.9970.292100
2.29-2.419.6240.21521.4738777197619760.9970.221100
2.4-2.5318.6380.1942335133188518850.9970.2100
2.53-2.6819.7320.15527.0934906176917690.9960.159100
2.68-2.8719.6980.12730.6733427169716970.9980.131100
2.87-3.118.6170.09635.5829284157315730.9980.099100
3.1-3.3917.2440.07339.8724918144514450.9990.075100
3.39-3.7917.8410.06146.2723461131513150.9990.063100
3.79-4.3817.1070.05349.420426119411940.9990.055100
4.38-5.3616.2390.0549.2316450101310130.9990.052100
5.36-7.5917.0280.04949.19134867937920.9990.05199.9
7.59-41.1815.6080.03950.9974454814770.9990.0499.2

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS21-Sep-2016data reduction
XDS21-Sep-2016data scaling
SHELXDphasing
SOLVEphasing
RESOLVEmodel building
SHELXEmodel building
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→41.18 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 1931 5.48 %
Rwork0.1516 33280 -
obs0.1528 35211 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.13 Å2 / Biso mean: 34.1078 Å2 / Biso min: 11.94 Å2
Refinement stepCycle: final / Resolution: 1.7→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 79 229 2200
Biso mean--27.71 38.41 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972003
X-RAY DIFFRACTIONf_angle_d1.1722715
X-RAY DIFFRACTIONf_chiral_restr0.0532288
X-RAY DIFFRACTIONf_plane_restr0.0065346
X-RAY DIFFRACTIONf_dihedral_angle_d14.7149739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.740.29361170.28341976209382
1.74-1.790.29111230.23142157228089
1.79-1.840.22941370.20052269240694
1.84-1.90.24321380.19052310244895
1.9-1.970.18651310.17472371250297
1.97-2.040.18131350.15252377251298
2.04-2.140.18671430.14332391253498
2.14-2.250.18431410.13732420256199
2.25-2.390.16031360.13172432256899
2.39-2.580.17081430.133924742617100
2.58-2.830.15181410.14424752616100
2.83-3.240.16731450.156624892634100
3.25-4.090.14671440.138225102654100
4.09-41.180.16241570.147826292786100
Refinement TLS params.Method: refined / Origin x: 35.066 Å / Origin y: 28.822 Å / Origin z: 12.045 Å
111213212223313233
T0.1151 Å20.0097 Å2-0.0114 Å2-0.1413 Å2-0.004 Å2--0.136 Å2
L1.3141 °20.0719 °20.2912 °2-0.7297 °20.1484 °2--2.2207 °2
S-0.0494 Å °0.0092 Å °0.0682 Å °-0.0147 Å °-0.02 Å °0.0504 Å °-0.1603 Å °0.0225 Å °0.0643 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 34:266 OR RESID 301:302 OR RESID 304 ) )A34 - 266
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 34:266 OR RESID 301:302 OR RESID 304 ) )A301 - 302
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 34:266 OR RESID 301:302 OR RESID 304 ) )A304

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