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

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Basic information

Entry
Database: PDB / ID: 6tes
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Glucuronic Acid
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-GLUCURONIC ACID / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 12, 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 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.occupancy / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,44710
Polymers82,7841
Non-polymers1,6639
Water7,981443
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)168,89420
Polymers165,5692
Non-polymers3,32618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area6980 Å2
ΔGint-47 kcal/mol
Surface area59310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.202, 100.505, 224.745
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-1238-

HOH

21A-1325-

HOH

31A-1503-

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 / Cell line (production host): HEK293F / 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, 450 molecules

#3: 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
#4: 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
#5: 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
#6: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H22N2O18P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 63.37 %
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-Glucuronic Acid
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.1 Å / Num. obs: 56604 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 26.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.566 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4537 / CC1/2: 0.86 / Rpim(I) all: 1.554 / % possible all: 98.6

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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: 2.2→49.1 Å / SU ML: 0.2624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4012
RfactorNum. reflection% reflection
Rfree0.238 2154 5.09 %
Rwork0.1904 40193 -
obs0.1928 42347 74.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5715 0 100 446 6261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746013
X-RAY DIFFRACTIONf_angle_d0.93938177
X-RAY DIFFRACTIONf_chiral_restr0.053858
X-RAY DIFFRACTIONf_plane_restr0.0061066
X-RAY DIFFRACTIONf_dihedral_angle_d18.063536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.5024970.45511533X-RAY DIFFRACTION44.07
2.25-2.310.4649790.36081718X-RAY DIFFRACTION48.31
2.31-2.370.4152950.2891732X-RAY DIFFRACTION48.59
2.37-2.440.2563920.22491741X-RAY DIFFRACTION48.97
2.44-2.520.2713960.23131855X-RAY DIFFRACTION51.87
2.52-2.610.29511100.23352057X-RAY DIFFRACTION57.99
2.61-2.710.32021210.23912375X-RAY DIFFRACTION66.83
2.71-2.840.28561640.24172590X-RAY DIFFRACTION73.28
2.84-2.990.27731580.22372994X-RAY DIFFRACTION83.65
2.99-3.170.29251810.22153420X-RAY DIFFRACTION95.01
3.17-3.420.21991780.19133568X-RAY DIFFRACTION99.92
3.42-3.760.25392030.18223558X-RAY DIFFRACTION98.92
3.76-4.310.17332080.14093601X-RAY DIFFRACTION99.84
4.31-5.420.16381770.12333683X-RAY DIFFRACTION99.97
5.42-49.10.18391950.1663768X-RAY DIFFRACTION99.45
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)
11.200081870380.5325299376160.4938812086841.25099160030.01002075728361.7047828641-0.06732162136360.2820313977730.00121879737934-0.2951940799740.0873026102563-0.0755749147913-0.290571191582-0.0108117788667-0.103166284310.3715800306240.04228030585850.08338462089890.197042649881-0.02107470446390.16769658250568.575259516431.6366755681146.71054781
20.9663166622760.1743417369120.2051553966321.02871081560.04158621239661.335658782670.04083919189050.197593474672-0.159599078982-0.1567741691320.106914712870.035796150297-0.00781960729684-0.307068330799-0.07189027780930.3392969444330.0608050634982-0.029546657840.185514058382-0.06375752862580.17295974991358.558295199821.5264466326149.376872114
31.06852077870.1726529464810.3362821787491.27617175899-0.4853970613170.6979945195860.157764428274-0.114360317786-0.02392876934330.147528351491-0.0898262173511-0.253149477923-0.14716640780.1261838850550.005042859309640.454149185247-0.0563072051575-0.08294164224580.202499026860.009350762774550.20754102432879.962054773238.9780235376189.770956841
41.028991157370.005949474277130.1629532895420.8786058577470.06890988075611.595966621270.0732768415349-0.0991517116307-0.07250987447970.0997051073724-0.0405903531197-0.01556893877490.029957457586-0.03113132348950.02245653456810.302974252629-0.00167854939006-0.04142446815280.08048084660450.03240313769090.16224673333470.582289214233.5418569458182.296454718
50.870771405566-0.2196426166390.9075401603141.72257515374-0.1826745964351.11709128781-0.0774224656677-0.241633492714-0.1504433925010.112641210551-0.04806717439370.0751718511512-0.3280816513110.2589750293410.03942721892080.473266126273-0.042993240675-0.03642867405270.3587953798890.1312824450030.20406504436578.457364579119.5835221661218.389860799
60.650226021794-0.378172712057-0.1601364169581.04844643846-0.432469849431.02818760026-0.0291461344326-0.172212332186-0.03724147596720.246247259027-0.0985589426816-0.128885664468-0.04267379291780.2737033815220.02300215429780.511319067348-0.0717554291172-0.06743329976860.4203621476410.1299697558870.19211349846781.175815602315.300338942223.257501083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 277 )
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 353 )
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 536 )
5X-RAY DIFFRACTION5chain 'A' and (resid 537 through 619 )
6X-RAY DIFFRACTION6chain 'A' and (resid 620 through 738 )

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