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- PDB-1t60: Crystal structure of Type IV collagen NC1 domain from bovine lens... -

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Basic information

Entry
Database: PDB / ID: 1t60
TitleCrystal structure of Type IV collagen NC1 domain from bovine lens capsule
Components(type iv collagen) x 2
KeywordsSTRUCTURAL PROTEIN / BASEMENT MEMBRANE / TYPE IV COLLAGEN / NC1 DOMAIN
Function / homology
Function and homology information


Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / Crosslinking of collagen fibrils / Laminin interactions / Non-integrin membrane-ECM interactions / Collagen degradation / extracellular matrix structural constituent conferring tensile strength ...Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Assembly of collagen fibrils and other multimeric structures / Integrin cell surface interactions / Crosslinking of collagen fibrils / Laminin interactions / Non-integrin membrane-ECM interactions / Collagen degradation / extracellular matrix structural constituent conferring tensile strength / collagen trimer / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / extracellular space / extracellular region
Similarity search - Function
Protein NDNF / Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) ...Protein NDNF / Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin fold / Beta Complex / Mainly Beta
Similarity search - Domain/homology
: / Collagen alpha-1(IV) chain / Collagen alpha-2(IV) chain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVanacore, R.M. / Shanmugasundararaj, S. / Friedman, D.B. / Bondar, O. / Hudson, B.G. / Sundaramoorthy, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The alpha1.alpha2 network of collagen IV. Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys cross-links
Authors: Vanacore, R.M. / Shanmugasundararaj, S. / Friedman, D.B. / Bondar, O. / Hudson, B.G. / Sundaramoorthy, M.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE A suitable database reference sequence could not be found for this structure at the time ...SEQUENCE A suitable database reference sequence could not be found for this structure at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: type iv collagen
B: type iv collagen
C: type iv collagen
D: type iv collagen
E: type iv collagen
F: type iv collagen
G: type iv collagen
H: type iv collagen
I: type iv collagen
J: type iv collagen
K: type iv collagen
L: type iv collagen
M: type iv collagen
N: type iv collagen
O: type iv collagen
P: type iv collagen
Q: type iv collagen
R: type iv collagen
S: type iv collagen
T: type iv collagen
U: type iv collagen
V: type iv collagen
W: type iv collagen
X: type iv collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)609,32365
Polymers607,06724
Non-polymers2,25641
Water51,1272838
1
A: type iv collagen
B: type iv collagen
C: type iv collagen
D: type iv collagen
E: type iv collagen
F: type iv collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,30116
Polymers151,7676
Non-polymers53510
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37670 Å2
ΔGint-264 kcal/mol
Surface area37630 Å2
MethodPISA
2
G: type iv collagen
H: type iv collagen
I: type iv collagen
J: type iv collagen
K: type iv collagen
L: type iv collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,18315
Polymers151,7676
Non-polymers4169
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37690 Å2
ΔGint-258 kcal/mol
Surface area37880 Å2
MethodPISA
3
M: type iv collagen
N: type iv collagen
O: type iv collagen
P: type iv collagen
Q: type iv collagen
R: type iv collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,41917
Polymers151,7676
Non-polymers65311
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38420 Å2
ΔGint-282 kcal/mol
Surface area37490 Å2
MethodPISA
4
S: type iv collagen
T: type iv collagen
U: type iv collagen
V: type iv collagen
W: type iv collagen
X: type iv collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,41917
Polymers151,7676
Non-polymers65311
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38710 Å2
ΔGint-267 kcal/mol
Surface area37310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.880, 140.129, 160.692
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 24 molecules ABDEGHJKMNPQSTVWCFILORUX

#1: Protein
type iv collagen


Mass: 25399.893 Da / Num. of mol.: 16 / Fragment: NC1 of alpha-1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: lens capsule / References: UniProt: Q7SIB2*PLUS
#2: Protein
type iv collagen


Mass: 25083.541 Da / Num. of mol.: 8 / Fragment: NC1 of alpha-2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: lens capsule / References: UniProt: Q7SIB3*PLUS

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Non-polymers , 4 types, 2879 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2838 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG20K, bicine, MPD, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.886 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2003
RadiationMonochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 859512 / Num. obs: 859512 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Rsym value: 0.075 / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1 / Rsym value: 0.68 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M3D

1m3d


Resolution: 1.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 31862 random
Rwork0.189 --
all0.209 797430 -
obs0.191 640828 -
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41657 0 32 2910 44599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d25.89
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.292 1695 -
Rwork0.275 --
obs-33782 5 %

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