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- PDB-5ze3: Crystal structure of human lysyl oxidase-like 2 (hLOXL2) in a pre... -

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Basic information

Entry
Database: PDB / ID: 5ze3
TitleCrystal structure of human lysyl oxidase-like 2 (hLOXL2) in a precursor state
ComponentsLysyl oxidase homolog 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


protein-lysine 6-oxidase / protein-lysine 6-oxidase activity / peptidyl-lysine oxidation / Crosslinking of collagen fibrils / heterochromatin organization / positive regulation of chondrocyte differentiation / oligosaccharide binding / negative regulation of stem cell population maintenance / Elastic fibre formation / collagen fibril organization ...protein-lysine 6-oxidase / protein-lysine 6-oxidase activity / peptidyl-lysine oxidation / Crosslinking of collagen fibrils / heterochromatin organization / positive regulation of chondrocyte differentiation / oligosaccharide binding / negative regulation of stem cell population maintenance / Elastic fibre formation / collagen fibril organization / response to copper ion / sprouting angiogenesis / endothelial cell proliferation / basement membrane / endothelial cell migration / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / protein modification process / collagen-containing extracellular matrix / response to hypoxia / copper ion binding / negative regulation of DNA-templated transcription / calcium ion binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / extracellular space / nucleoplasm / membrane / nucleus
Similarity search - Function
Lysyl oxidase / Lysyl oxidase, conserved site / : / Lysyl oxidase / Lysyl oxidase putative copper-binding region signature. / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain ...Lysyl oxidase / Lysyl oxidase, conserved site / : / Lysyl oxidase / Lysyl oxidase putative copper-binding region signature. / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich
Similarity search - Domain/homology
Lysyl oxidase homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsZhang, X. / Liu, M.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2014ZX09507003006 to Y.S. China
National Natural Science Foundation of China31130002 and 31321062 to Y.S. China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structure of human lysyl oxidase-like 2 (hLOXL2) in a precursor state.
Authors: Zhang, X. / Wang, Q. / Wu, J. / Wang, J. / Shi, Y. / Liu, M.
History
DepositionFeb 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysyl oxidase homolog 2
B: Lysyl oxidase homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0289
Polymers102,2782
Non-polymers7497
Water3,639202
1
A: Lysyl oxidase homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4664
Polymers51,1391
Non-polymers3273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint2 kcal/mol
Surface area20950 Å2
MethodPISA
2
B: Lysyl oxidase homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5625
Polymers51,1391
Non-polymers4234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-9 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.095, 61.487, 137.883
Angle α, β, γ (deg.)90.00, 102.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Lysyl oxidase homolog 2 / Lysyl oxidase-like protein 2 / Lysyl oxidase-related protein 2 / Lysyl oxidase-related protein WS9-14


Mass: 51139.059 Da / Num. of mol.: 2 / Mutation: N455Q,M570L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LOXL2 / Production host: Homo sapiens (human) / References: UniProt: Q9Y4K0, protein-lysine 6-oxidase
#3: 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.: 2
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 , 4 types, 207 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 28% PEG 2000, 100mM Li2SO4, 100mM HEPES, pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: MPCCD / Detector: CCD / Date: Apr 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45694 / % possible obs: 98 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.86
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.04 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2405: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementResolution: 2.4→36.497 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.15
RfactorNum. reflection% reflection
Rfree0.2391 2212 5.08 %
Rwork0.2171 --
obs0.2182 43539 85.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→36.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 37 202 7153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117128
X-RAY DIFFRACTIONf_angle_d1.6319660
X-RAY DIFFRACTIONf_dihedral_angle_d27.0282634
X-RAY DIFFRACTIONf_chiral_restr0.085996
X-RAY DIFFRACTIONf_plane_restr0.011282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3372-2.3880.2818750.25031427X-RAY DIFFRACTION48
2.388-2.44360.2888720.27041667X-RAY DIFFRACTION55
2.4436-2.50460.29041060.26521841X-RAY DIFFRACTION62
2.5046-2.57230.3147990.2712041X-RAY DIFFRACTION68
2.5723-2.6480.28161180.25832227X-RAY DIFFRACTION74
2.648-2.73350.28741120.26492396X-RAY DIFFRACTION79
2.7335-2.83110.30821490.26372645X-RAY DIFFRACTION88
2.8311-2.94440.28361440.26952929X-RAY DIFFRACTION96
2.9444-3.07840.28731560.27993023X-RAY DIFFRACTION99
3.0784-3.24060.30481580.25262981X-RAY DIFFRACTION100
3.2406-3.44350.29251760.24153008X-RAY DIFFRACTION100
3.4435-3.70910.25011710.20842979X-RAY DIFFRACTION99
3.7091-4.08190.19921840.19293023X-RAY DIFFRACTION99
4.0819-4.67150.17461560.16862987X-RAY DIFFRACTION99
4.6715-5.88170.17991690.17163034X-RAY DIFFRACTION99
5.8817-36.50130.19591670.17963119X-RAY DIFFRACTION99
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)
11.3716-0.57980.0183.5318-1.1662.71340.08830.0711-0.0856-0.1373-0.1041-0.05530.15620.2945-0.00610.10470.0219-0.04030.21560.00260.287218.125-17.055659.268
23.11971.3357-0.71190.9437-0.25430.7938-0.05610.20090.4482-0.19620.11780.2283-0.1993-0.0147-0.07120.25810.0163-0.01530.14150.00550.21681.86966.395352.0552
32.88480.41820.50482.39890.55312.3686-0.04720.2181-0.0632-0.13520.06150.02080.20060.0339-0.01050.0957-0.010.0010.13350.04240.1349-8.3187-7.158657.381
42.3371-0.03640.85914.1863-0.70821.4047-0.0102-0.06830.3461-0.09560.0004-0.2882-0.23630.13920.08170.7899-0.11550.12430.4269-0.07030.361138.426531.29734.3966
50.63720.3383-0.55160.8427-1.59563.03020.04830.0986-0.059-0.62410.01580.02860.1353-0.01120.02831.0001-0.03610.08570.3852-0.0320.291326.14556.934821.6095
61.04140.4411-0.59561.0077-0.35362.90010.04870.28820.1646-0.48670.04260.2262-0.2586-0.4119-0.36041.3477-0.06170.19680.50020.07920.225528.552822.87948.3662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 322 through 434 )
2X-RAY DIFFRACTION2chain 'A' and (resid 435 through 605 )
3X-RAY DIFFRACTION3chain 'A' and (resid 606 through 762 )
4X-RAY DIFFRACTION4chain 'B' and (resid 321 through 435 )
5X-RAY DIFFRACTION5chain 'B' and (resid 436 through 590 )
6X-RAY DIFFRACTION6chain 'B' and (resid 591 through 763 )

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