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- PDB-1bnl: ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN -

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Basic information

Entry
Database: PDB / ID: 1bnl
TitleZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN
ComponentsCOLLAGEN XVIII
KeywordsEXTRACELLULAR MATRIX / ENDOSTATIN / COLLAGEN XVIII / COLLAGEN / ANTIANGIOGENIC / ANGIOGENIC / ANGIOGENISIS / CANCER / ZINC
Function / homology
Function and homology information


response to hydrostatic pressure / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / endothelial cell morphogenesis / Laminin interactions / collagen trimer / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation ...response to hydrostatic pressure / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / endothelial cell morphogenesis / Laminin interactions / collagen trimer / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / basement membrane / Integrin cell surface interactions / visual perception / animal organ morphogenesis / skeletal system development / : / angiogenesis / cell adhesion / response to xenobiotic stimulus / endoplasmic reticulum lumen / negative regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Domain of Unknown Function (DUF959) / Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / : ...Domain of unknown function DUF959, collagen XVIII, N-terminal / Collagen alpha-1(XVIII) chain, frizzled domain / Domain of Unknown Function (DUF959) / Collagenase NC10/endostatin / Collagen type XV/XVIII, trimerization domain / Collagenase NC10 and Endostatin / Collagen trimerization domain / : / Thrombospondin N-terminal -like domains. / : / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Concanavalin A-like lectin/glucanase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Collagen alpha-1(XVIII) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDing, Y.-H. / Javaherian, K. / Lo, K.-M. / Chopra, R. / Boehm, T. / Lanciotti, J. / Harris, B.A. / Li, Y. / Shapiro, R. / Hohenester, E. ...Ding, Y.-H. / Javaherian, K. / Lo, K.-M. / Chopra, R. / Boehm, T. / Lanciotti, J. / Harris, B.A. / Li, Y. / Shapiro, R. / Hohenester, E. / Timpl, R. / Folkman, J. / Wiley, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Zinc-dependent dimers observed in crystals of human endostatin.
Authors: Ding, Y.H. / Javaherian, K. / Lo, K.M. / Chopra, R. / Boehm, T. / Lanciotti, J. / Harris, B.A. / Li, Y. / Shapiro, R. / Hohenester, E. / Timpl, R. / Folkman, J. / Wiley, D.C.
History
DepositionJul 30, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGEN XVIII
B: COLLAGEN XVIII
C: COLLAGEN XVIII
D: COLLAGEN XVIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6108
Polymers78,3494
Non-polymers2624
Water00
1
A: COLLAGEN XVIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6532
Polymers19,5871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COLLAGEN XVIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6532
Polymers19,5871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: COLLAGEN XVIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6532
Polymers19,5871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: COLLAGEN XVIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6532
Polymers19,5871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.713, 74.266, 137.805
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.969256, -0.033237, 0.243799), (0.003878, -0.992775, -0.119928), (0.246023, -0.115296, 0.962382)46.67916, 42.61212, -3.29596
2given(0.999851, 0.004599, 0.01662), (0.004597, -0.99999, 0.000159), (0.016621, -8.2E-5, -0.999862)31.00356, 38.42128, 66.99419
3given(-0.97465, -0.021891, 0.22266), (0.003764, 0.993456, 0.114151), (-0.223702, 0.112096, -0.96819)78.53633, -4.21531, 70.21631

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Components

#1: Protein
COLLAGEN XVIII


Mass: 19587.172 Da / Num. of mol.: 4
Fragment: ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: SECRETED / Gene: COLLAGEN XVIII / Plasmid: PDCS-FC(D4K) / Production host: NS/0 MURINE MYELOMA CELLS / References: UniProt: P39060
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
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 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
3150 mM1reservoirNaCl
450 mMTris-HCl1reservoir
56 %PEG80001reservoir
61.5 M1reservoirNaCl
72 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorDetector: CCD / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 19089 / % possible obs: 89.9 % / Redundancy: 2.9 % / Rsym value: 0.071 / Net I/σ(I): 14.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.138 / % possible all: 59
Reflection
*PLUS
Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 59 % / Num. unique obs: 1336 / Rmerge(I) obs: 0.138

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1272 7.5 %RANDOM
Rwork0.24 ---
obs0.24 18175 89.9 %-
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 4 0 5532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.03
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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