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- PDB-6tec: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Co... -

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Basic information

Entry
Database: PDB / ID: 6tec
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Xylose
ComponentsProcollagen-lysine,2-oxoglutarate 5-dioxygenase 3
KeywordsTRANSFERASE / Collagen / lysyl hydroxylase / hydroxylysine / galactosyltransferase / glucosyltransferase
Function / homology
Function and homology information


procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen galactosyltransferase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / basement membrane assembly / epidermis morphogenesis ...procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen galactosyltransferase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / collagen fibril organization / L-ascorbic acid binding / neural tube development / small molecule binding / lung morphogenesis / rough endoplasmic reticulum / trans-Golgi network / vasodilation / intracellular protein localization / : / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / PLOD GT domain / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase ...Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / PLOD GT domain / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChiapparino, A. / De Giorgi, F. / Scietti, L. / Faravelli, S. / Roscioli, T. / Forneris, F.
Funding support Italy, 4items
OrganizationGrant numberCountry
European CommissionMSCA-IF 745934 - COTETHERS
Italian Association for Cancer Research20075 Italy
Other privateThe Giovanni Armenise-Harvard Foundation CDA 2013 Italy
Italian Ministry of EducationDipartimenti di Eccellenza Program 2018-2022 Italy
CitationJournal: Int J Mol Sci / Year: 2023
Title: Identification of Regulatory Molecular 'Hot Spots' for LH/PLOD Collagen Glycosyltransferase Activity
Authors: Mattoteia, D. / Chiapparino, A. / Fumagalli, M. / De Marco, M. / De Giorgi, F. / Negro, L. / Pinnola, A. / Faravelli, S. / Roscioli, T. / Scietti, L. / Forneris, F.
History
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,52712
Polymers82,7841
Non-polymers1,74311
Water2,864159
1
A: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
hetero molecules

A: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,05524
Polymers165,5692
Non-polymers3,48622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area7670 Å2
ΔGint-31 kcal/mol
Surface area58850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.264, 99.987, 223.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-952-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 / Lysyl hydroxylase 3 / LH3


Mass: 82784.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First Ser residue and last three Ala residues were introduced by molecular cloning
Source: (gene. exp.) Homo sapiens (human) / Gene: PLOD3 / Production host: Homo sapiens (human)
References: UniProt: O60568, procollagen-lysine 5-dioxygenase, procollagen galactosyltransferase, procollagen glucosyltransferase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 168 molecules

#3: Chemical ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 600 mM sodium formate, 12% PGA-LM, 100 mM HEPES/NaOH, 500 uM FeCl2, 500 uM MnCl2, 1 mM UDP-Xylose
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→48.79 Å / Num. obs: 43005 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.48 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.147 / Net I/σ(I): 5.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.831 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 4500 / CC1/2: 0.586 / Rpim(I) all: 1.274 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FXK

6fxk


Resolution: 2.4→48.79 Å / SU ML: 0.2203 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7098
RfactorNum. reflection% reflection
Rfree0.2159 1300 4.78 %
Rwork0.1852 --
obs0.1867 27202 63.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 105 160 5980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196026
X-RAY DIFFRACTIONf_angle_d0.51488191
X-RAY DIFFRACTIONf_chiral_restr0.0424858
X-RAY DIFFRACTIONf_plane_restr0.00421067
X-RAY DIFFRACTIONf_dihedral_angle_d16.94643545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.2706280.2415459X-RAY DIFFRACTION10.26
2.5-2.610.2626360.2861673X-RAY DIFFRACTION15.15
2.61-2.750.2715720.27091218X-RAY DIFFRACTION27.39
2.75-2.920.291150.26192226X-RAY DIFFRACTION49.15
2.92-3.150.28561540.25193244X-RAY DIFFRACTION71.42
3.15-3.460.25151970.20754226X-RAY DIFFRACTION93
3.46-3.960.2232140.17484549X-RAY DIFFRACTION99.87
3.96-4.990.16852320.14254614X-RAY DIFFRACTION99.65
4.99-48.790.18482520.16514693X-RAY DIFFRACTION99.4
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)
10.159558458360.04261975951320.04385331726260.05995262193870.03801610372410.07872512461580.02072261837860.0915908559526-0.0156994614762-0.0598852304851-0.0194847037335-0.00590857721337-0.09149770772820.004977366817150.0190905250950.06645682141460.02399062149820.004993627972350.07017341917490.008644948497070.032511330302767.978371475329.052027777145.989912533
20.02528154925280.00707137531665-0.05169977293940.00219855691552-0.01393423458730.1075759325140.02135179107470.0579651146125-0.00243867983666-0.0760079090238-0.04627568986290.065257395115-0.0568407221405-0.1039353871260.06870581926630.06818869347740.0531769690337-0.05332284681940.0752625094309-0.03699263623120.053949099834557.051746775122.074350067149.08303219
30.02168654208420.00838745556506-0.01126803470780.0586194893844-0.009767314564430.006311020722080.0351994947159-0.03589127976580.007902865548160.0749230522094-0.0341379483153-0.03842595225370.01150836568760.008381774636990.004740217112430.0674015659948-0.0300308676178-0.02975242947130.04154302206710.006327014731710.10136122863677.051038779641.6552145294187.164499983
40.0150790507477-0.00151135944052-0.02254307498930.0007246597672960.003185909823920.0356616312976-0.00106723067470.0122940571497-0.0001845878748510.0001047058765230.01099864791520.008387428747790.0166501477893-0.02984153120680.03234759169760.0228389887941-0.012871570607-0.01116729553810.03065247795010.01852116690460.084913674833868.698637287430.8366685239177.069032084
50.01314941304580.0159861280111-0.007356691793220.0216947425317-0.01178100181760.006939048012850.0312374865303-0.0330362873504-0.007781306034150.0566284855823-0.006412897957560.00275252051090.00615429423509-0.007563630614780.007371592319530.101347404051-0.0194528314211-0.01797974929360.07317150204580.04324232421720.069777027746670.168191231727.7059970704193.054841208
60.00659724250126-0.00103811713407-0.007429356647490.0079123428994-0.009310874410760.0242030663521-0.00989911884209-0.01764316445190.007573184082680.0606267505089-0.0319873493613-0.0234776785348-0.01382688754540.0917173479751-0.03247167411030.226319754295-0.0537033232551-0.02697762482410.1475422844530.04828985358080.071205943712479.133337667417.0722984138220.409334478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 277 )
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 392 )
4X-RAY DIFFRACTION4chain 'A' and (resid 393 through 500 )
5X-RAY DIFFRACTION5chain 'A' and (resid 501 through 536 )
6X-RAY DIFFRACTION6chain 'A' and (resid 537 through 738 )

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